EnsDb-seqlevels.RdThe methods and functions on this help page allow to integrate
EnsDb objects and the annotations they provide with other
Bioconductor annotation packages that base on chromosome names
(seqlevels) that are different from those defined by Ensembl.
# S4 method for EnsDb
seqlevelsStyle(x)
# S4 method for EnsDb
seqlevelsStyle(x) <- value
# S4 method for EnsDb
supportedSeqlevelsStyles(x)(In alphabetic order)
For seqlevelsStyle<-: a character string specifying the
seqlevels style that should be set. Use the
supportedSeqlevelsStyle to list all available and supported
seqlevel styles. As an alternative, it is also possible to submit a
data.frame with custom mapping. This needs to have two
columns, one of them being called "Ensembl" with the original
chromosome names and another column with the new names.
An EnsDb instance.
Get the style of the seqlevels in which results returned from the
EnsDb object are encoded. By default, and internally,
seqnames as provided by Ensembl are used.
The method returns a character string specifying the currently used seqlevelstyle.
Change the style of the seqlevels in which results returned from
the EnsDb object are encoded. Changing the seqlevels helps
integrating annotations from EnsDb objects e.g. with
annotations from packages that base on UCSC annotations. The
function also supports using/defining custom mappings by
submitting a mapping data.frame (see examples below).
Lists all seqlevel styles for which mappings between seqlevel
styles are available in the GenomeInfoDb package.
The method returns a character vector with supported seqlevel
styles for the organism of the EnsDb object.
The mapping between different seqname styles is performed based on
data provided by the GenomeInfoDb package. Note that in most
instances no mapping is provided for seqnames other than for primary
chromosomes. By default functions from the ensembldb package
return the original seqname is in such cases. This behaviour
can be changed with the ensembldb.seqnameNotFound global
option. For the special keyword "ORIGINAL" (the default), the
original seqnames are returned, for "MISSING" an error is
thrown if a seqname can not be mapped. In all other cases, the value
of the option is returned as seqname if no mapping is available
(e.g. setting options(ensembldb.seqnameNotFound=NA) returns an
NA if the seqname is not mappable).
For seqlevelsStyle: see method description above.
For supportedSeqlevelsStyles: see method description above.
library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86
## Get the internal, default seqlevel style.
seqlevelsStyle(edb)
#> [1] "Ensembl"
## Get the seqlevels from the database.
seqlevels(edb)
#> [1] "1"
#> [2] "10"
#> [3] "11"
#> [4] "12"
#> [5] "13"
#> [6] "14"
#> [7] "15"
#> [8] "16"
#> [9] "17"
#> [10] "18"
#> [11] "19"
#> [12] "2"
#> [13] "20"
#> [14] "21"
#> [15] "22"
#> [16] "3"
#> [17] "4"
#> [18] "5"
#> [19] "6"
#> [20] "7"
#> [21] "8"
#> [22] "9"
#> [23] "CHR_HG107_PATCH"
#> [24] "CHR_HG126_PATCH"
#> [25] "CHR_HG1311_PATCH"
#> [26] "CHR_HG1342_HG2282_PATCH"
#> [27] "CHR_HG1362_PATCH"
#> [28] "CHR_HG142_HG150_NOVEL_TEST"
#> [29] "CHR_HG151_NOVEL_TEST"
#> [30] "CHR_HG1651_PATCH"
#> [31] "CHR_HG1832_PATCH"
#> [32] "CHR_HG2021_PATCH"
#> [33] "CHR_HG2022_PATCH"
#> [34] "CHR_HG2023_PATCH"
#> [35] "CHR_HG2030_PATCH"
#> [36] "CHR_HG2058_PATCH"
#> [37] "CHR_HG2062_PATCH"
#> [38] "CHR_HG2063_PATCH"
#> [39] "CHR_HG2066_PATCH"
#> [40] "CHR_HG2072_PATCH"
#> [41] "CHR_HG2095_PATCH"
#> [42] "CHR_HG2104_PATCH"
#> [43] "CHR_HG2116_PATCH"
#> [44] "CHR_HG2128_PATCH"
#> [45] "CHR_HG2191_PATCH"
#> [46] "CHR_HG2213_PATCH"
#> [47] "CHR_HG2217_PATCH"
#> [48] "CHR_HG2232_PATCH"
#> [49] "CHR_HG2233_PATCH"
#> [50] "CHR_HG2235_PATCH"
#> [51] "CHR_HG2239_PATCH"
#> [52] "CHR_HG2247_PATCH"
#> [53] "CHR_HG2249_PATCH"
#> [54] "CHR_HG2288_HG2289_PATCH"
#> [55] "CHR_HG2290_PATCH"
#> [56] "CHR_HG2291_PATCH"
#> [57] "CHR_HG2334_PATCH"
#> [58] "CHR_HG26_PATCH"
#> [59] "CHR_HG986_PATCH"
#> [60] "CHR_HSCHR10_1_CTG1"
#> [61] "CHR_HSCHR10_1_CTG2"
#> [62] "CHR_HSCHR10_1_CTG3"
#> [63] "CHR_HSCHR10_1_CTG4"
#> [64] "CHR_HSCHR10_1_CTG6"
#> [65] "CHR_HSCHR11_1_CTG1_2"
#> [66] "CHR_HSCHR11_1_CTG5"
#> [67] "CHR_HSCHR11_1_CTG6"
#> [68] "CHR_HSCHR11_1_CTG7"
#> [69] "CHR_HSCHR11_1_CTG8"
#> [70] "CHR_HSCHR11_2_CTG1"
#> [71] "CHR_HSCHR11_2_CTG1_1"
#> [72] "CHR_HSCHR11_3_CTG1"
#> [73] "CHR_HSCHR12_1_CTG1"
#> [74] "CHR_HSCHR12_1_CTG2_1"
#> [75] "CHR_HSCHR12_2_CTG1"
#> [76] "CHR_HSCHR12_2_CTG2"
#> [77] "CHR_HSCHR12_2_CTG2_1"
#> [78] "CHR_HSCHR12_3_CTG2"
#> [79] "CHR_HSCHR12_3_CTG2_1"
#> [80] "CHR_HSCHR12_4_CTG2"
#> [81] "CHR_HSCHR12_4_CTG2_1"
#> [82] "CHR_HSCHR12_5_CTG2"
#> [83] "CHR_HSCHR12_5_CTG2_1"
#> [84] "CHR_HSCHR12_6_CTG2_1"
#> [85] "CHR_HSCHR13_1_CTG1"
#> [86] "CHR_HSCHR13_1_CTG3"
#> [87] "CHR_HSCHR13_1_CTG5"
#> [88] "CHR_HSCHR13_1_CTG8"
#> [89] "CHR_HSCHR14_1_CTG1"
#> [90] "CHR_HSCHR14_2_CTG1"
#> [91] "CHR_HSCHR14_3_CTG1"
#> [92] "CHR_HSCHR14_7_CTG1"
#> [93] "CHR_HSCHR15_1_CTG1"
#> [94] "CHR_HSCHR15_1_CTG3"
#> [95] "CHR_HSCHR15_1_CTG8"
#> [96] "CHR_HSCHR15_2_CTG3"
#> [97] "CHR_HSCHR15_2_CTG8"
#> [98] "CHR_HSCHR15_3_CTG3"
#> [99] "CHR_HSCHR15_3_CTG8"
#> [100] "CHR_HSCHR15_4_CTG8"
#> [101] "CHR_HSCHR15_5_CTG8"
#> [102] "CHR_HSCHR15_6_CTG8"
#> [103] "CHR_HSCHR16_1_CTG1"
#> [104] "CHR_HSCHR16_1_CTG3_1"
#> [105] "CHR_HSCHR16_2_CTG3_1"
#> [106] "CHR_HSCHR16_3_CTG1"
#> [107] "CHR_HSCHR16_4_CTG1"
#> [108] "CHR_HSCHR16_4_CTG3_1"
#> [109] "CHR_HSCHR16_5_CTG1"
#> [110] "CHR_HSCHR16_CTG2"
#> [111] "CHR_HSCHR17_10_CTG4"
#> [112] "CHR_HSCHR17_1_CTG1"
#> [113] "CHR_HSCHR17_1_CTG2"
#> [114] "CHR_HSCHR17_1_CTG4"
#> [115] "CHR_HSCHR17_1_CTG5"
#> [116] "CHR_HSCHR17_1_CTG9"
#> [117] "CHR_HSCHR17_2_CTG1"
#> [118] "CHR_HSCHR17_2_CTG2"
#> [119] "CHR_HSCHR17_2_CTG4"
#> [120] "CHR_HSCHR17_2_CTG5"
#> [121] "CHR_HSCHR17_3_CTG2"
#> [122] "CHR_HSCHR17_3_CTG4"
#> [123] "CHR_HSCHR17_4_CTG4"
#> [124] "CHR_HSCHR17_5_CTG4"
#> [125] "CHR_HSCHR17_6_CTG4"
#> [126] "CHR_HSCHR17_7_CTG4"
#> [127] "CHR_HSCHR17_8_CTG4"
#> [128] "CHR_HSCHR17_9_CTG4"
#> [129] "CHR_HSCHR18_1_CTG1_1"
#> [130] "CHR_HSCHR18_1_CTG2_1"
#> [131] "CHR_HSCHR18_2_CTG1_1"
#> [132] "CHR_HSCHR18_2_CTG2"
#> [133] "CHR_HSCHR18_2_CTG2_1"
#> [134] "CHR_HSCHR18_3_CTG2_1"
#> [135] "CHR_HSCHR18_5_CTG1_1"
#> [136] "CHR_HSCHR18_ALT21_CTG2_1"
#> [137] "CHR_HSCHR18_ALT2_CTG2_1"
#> [138] "CHR_HSCHR19KIR_ABC08_A1_HAP_CTG3_1"
#> [139] "CHR_HSCHR19KIR_ABC08_AB_HAP_C_P_CTG3_1"
#> [140] "CHR_HSCHR19KIR_ABC08_AB_HAP_T_P_CTG3_1"
#> [141] "CHR_HSCHR19KIR_FH05_A_HAP_CTG3_1"
#> [142] "CHR_HSCHR19KIR_FH05_B_HAP_CTG3_1"
#> [143] "CHR_HSCHR19KIR_FH06_A_HAP_CTG3_1"
#> [144] "CHR_HSCHR19KIR_FH06_BA1_HAP_CTG3_1"
#> [145] "CHR_HSCHR19KIR_FH08_A_HAP_CTG3_1"
#> [146] "CHR_HSCHR19KIR_FH08_BAX_HAP_CTG3_1"
#> [147] "CHR_HSCHR19KIR_FH13_A_HAP_CTG3_1"
#> [148] "CHR_HSCHR19KIR_FH13_BA2_HAP_CTG3_1"
#> [149] "CHR_HSCHR19KIR_FH15_A_HAP_CTG3_1"
#> [150] "CHR_HSCHR19KIR_FH15_B_HAP_CTG3_1"
#> [151] "CHR_HSCHR19KIR_G085_A_HAP_CTG3_1"
#> [152] "CHR_HSCHR19KIR_G085_BA1_HAP_CTG3_1"
#> [153] "CHR_HSCHR19KIR_G248_A_HAP_CTG3_1"
#> [154] "CHR_HSCHR19KIR_G248_BA2_HAP_CTG3_1"
#> [155] "CHR_HSCHR19KIR_GRC212_AB_HAP_CTG3_1"
#> [156] "CHR_HSCHR19KIR_GRC212_BA1_HAP_CTG3_1"
#> [157] "CHR_HSCHR19KIR_LUCE_A_HAP_CTG3_1"
#> [158] "CHR_HSCHR19KIR_LUCE_BDEL_HAP_CTG3_1"
#> [159] "CHR_HSCHR19KIR_RP5_B_HAP_CTG3_1"
#> [160] "CHR_HSCHR19KIR_RSH_A_HAP_CTG3_1"
#> [161] "CHR_HSCHR19KIR_RSH_BA2_HAP_CTG3_1"
#> [162] "CHR_HSCHR19KIR_T7526_A_HAP_CTG3_1"
#> [163] "CHR_HSCHR19KIR_T7526_BDEL_HAP_CTG3_1"
#> [164] "CHR_HSCHR19LRC_COX1_CTG3_1"
#> [165] "CHR_HSCHR19LRC_COX2_CTG3_1"
#> [166] "CHR_HSCHR19LRC_LRC_I_CTG3_1"
#> [167] "CHR_HSCHR19LRC_LRC_J_CTG3_1"
#> [168] "CHR_HSCHR19LRC_LRC_S_CTG3_1"
#> [169] "CHR_HSCHR19LRC_LRC_T_CTG3_1"
#> [170] "CHR_HSCHR19LRC_PGF1_CTG3_1"
#> [171] "CHR_HSCHR19LRC_PGF2_CTG3_1"
#> [172] "CHR_HSCHR19_1_CTG2"
#> [173] "CHR_HSCHR19_1_CTG3_1"
#> [174] "CHR_HSCHR19_2_CTG2"
#> [175] "CHR_HSCHR19_2_CTG3_1"
#> [176] "CHR_HSCHR19_3_CTG2"
#> [177] "CHR_HSCHR19_3_CTG3_1"
#> [178] "CHR_HSCHR19_4_CTG2"
#> [179] "CHR_HSCHR19_4_CTG3_1"
#> [180] "CHR_HSCHR19_5_CTG2"
#> [181] "CHR_HSCHR1_1_CTG11"
#> [182] "CHR_HSCHR1_1_CTG3"
#> [183] "CHR_HSCHR1_1_CTG31"
#> [184] "CHR_HSCHR1_1_CTG32_1"
#> [185] "CHR_HSCHR1_2_CTG3"
#> [186] "CHR_HSCHR1_2_CTG31"
#> [187] "CHR_HSCHR1_2_CTG32_1"
#> [188] "CHR_HSCHR1_3_CTG3"
#> [189] "CHR_HSCHR1_3_CTG31"
#> [190] "CHR_HSCHR1_3_CTG32_1"
#> [191] "CHR_HSCHR1_4_CTG3"
#> [192] "CHR_HSCHR1_4_CTG31"
#> [193] "CHR_HSCHR1_5_CTG3"
#> [194] "CHR_HSCHR1_5_CTG32_1"
#> [195] "CHR_HSCHR1_ALT2_1_CTG32_1"
#> [196] "CHR_HSCHR20_1_CTG1"
#> [197] "CHR_HSCHR20_1_CTG2"
#> [198] "CHR_HSCHR20_1_CTG3"
#> [199] "CHR_HSCHR20_1_CTG4"
#> [200] "CHR_HSCHR21_2_CTG1_1"
#> [201] "CHR_HSCHR21_3_CTG1_1"
#> [202] "CHR_HSCHR21_4_CTG1_1"
#> [203] "CHR_HSCHR21_5_CTG2"
#> [204] "CHR_HSCHR21_6_CTG1_1"
#> [205] "CHR_HSCHR21_8_CTG1_1"
#> [206] "CHR_HSCHR22_1_CTG1"
#> [207] "CHR_HSCHR22_1_CTG2"
#> [208] "CHR_HSCHR22_1_CTG3"
#> [209] "CHR_HSCHR22_1_CTG4"
#> [210] "CHR_HSCHR22_1_CTG5"
#> [211] "CHR_HSCHR22_1_CTG6"
#> [212] "CHR_HSCHR22_1_CTG7"
#> [213] "CHR_HSCHR22_2_CTG1"
#> [214] "CHR_HSCHR22_3_CTG1"
#> [215] "CHR_HSCHR22_4_CTG1"
#> [216] "CHR_HSCHR22_5_CTG1"
#> [217] "CHR_HSCHR22_6_CTG1"
#> [218] "CHR_HSCHR22_7_CTG1"
#> [219] "CHR_HSCHR22_8_CTG1"
#> [220] "CHR_HSCHR2_1_CTG1"
#> [221] "CHR_HSCHR2_1_CTG15"
#> [222] "CHR_HSCHR2_1_CTG5"
#> [223] "CHR_HSCHR2_1_CTG7"
#> [224] "CHR_HSCHR2_1_CTG7_2"
#> [225] "CHR_HSCHR2_2_CTG1"
#> [226] "CHR_HSCHR2_2_CTG15"
#> [227] "CHR_HSCHR2_2_CTG7"
#> [228] "CHR_HSCHR2_2_CTG7_2"
#> [229] "CHR_HSCHR2_3_CTG1"
#> [230] "CHR_HSCHR2_3_CTG15"
#> [231] "CHR_HSCHR2_3_CTG7_2"
#> [232] "CHR_HSCHR2_4_CTG1"
#> [233] "CHR_HSCHR2_6_CTG7_2"
#> [234] "CHR_HSCHR3_1_CTG1"
#> [235] "CHR_HSCHR3_1_CTG2_1"
#> [236] "CHR_HSCHR3_1_CTG3"
#> [237] "CHR_HSCHR3_2_CTG2_1"
#> [238] "CHR_HSCHR3_2_CTG3"
#> [239] "CHR_HSCHR3_3_CTG1"
#> [240] "CHR_HSCHR3_3_CTG3"
#> [241] "CHR_HSCHR3_4_CTG2_1"
#> [242] "CHR_HSCHR3_4_CTG3"
#> [243] "CHR_HSCHR3_5_CTG2_1"
#> [244] "CHR_HSCHR3_5_CTG3"
#> [245] "CHR_HSCHR3_6_CTG3"
#> [246] "CHR_HSCHR3_7_CTG3"
#> [247] "CHR_HSCHR3_8_CTG3"
#> [248] "CHR_HSCHR3_9_CTG3"
#> [249] "CHR_HSCHR4_11_CTG12"
#> [250] "CHR_HSCHR4_1_CTG12"
#> [251] "CHR_HSCHR4_1_CTG4"
#> [252] "CHR_HSCHR4_1_CTG6"
#> [253] "CHR_HSCHR4_1_CTG9"
#> [254] "CHR_HSCHR4_2_CTG12"
#> [255] "CHR_HSCHR4_2_CTG4"
#> [256] "CHR_HSCHR4_3_CTG12"
#> [257] "CHR_HSCHR4_4_CTG12"
#> [258] "CHR_HSCHR4_5_CTG12"
#> [259] "CHR_HSCHR4_6_CTG12"
#> [260] "CHR_HSCHR4_7_CTG12"
#> [261] "CHR_HSCHR4_8_CTG12"
#> [262] "CHR_HSCHR4_9_CTG12"
#> [263] "CHR_HSCHR5_1_CTG1"
#> [264] "CHR_HSCHR5_1_CTG1_1"
#> [265] "CHR_HSCHR5_1_CTG5"
#> [266] "CHR_HSCHR5_2_CTG1"
#> [267] "CHR_HSCHR5_2_CTG1_1"
#> [268] "CHR_HSCHR5_2_CTG5"
#> [269] "CHR_HSCHR5_3_CTG1"
#> [270] "CHR_HSCHR5_3_CTG5"
#> [271] "CHR_HSCHR5_4_CTG1"
#> [272] "CHR_HSCHR5_4_CTG1_1"
#> [273] "CHR_HSCHR5_5_CTG1"
#> [274] "CHR_HSCHR5_6_CTG1"
#> [275] "CHR_HSCHR5_7_CTG1"
#> [276] "CHR_HSCHR6_1_CTG10"
#> [277] "CHR_HSCHR6_1_CTG2"
#> [278] "CHR_HSCHR6_1_CTG3"
#> [279] "CHR_HSCHR6_1_CTG4"
#> [280] "CHR_HSCHR6_1_CTG5"
#> [281] "CHR_HSCHR6_1_CTG6"
#> [282] "CHR_HSCHR6_1_CTG7"
#> [283] "CHR_HSCHR6_1_CTG8"
#> [284] "CHR_HSCHR6_1_CTG9"
#> [285] "CHR_HSCHR6_8_CTG1"
#> [286] "CHR_HSCHR6_MHC_APD_CTG1"
#> [287] "CHR_HSCHR6_MHC_COX_CTG1"
#> [288] "CHR_HSCHR6_MHC_DBB_CTG1"
#> [289] "CHR_HSCHR6_MHC_MANN_CTG1"
#> [290] "CHR_HSCHR6_MHC_MCF_CTG1"
#> [291] "CHR_HSCHR6_MHC_QBL_CTG1"
#> [292] "CHR_HSCHR6_MHC_SSTO_CTG1"
#> [293] "CHR_HSCHR7_1_CTG1"
#> [294] "CHR_HSCHR7_1_CTG4_4"
#> [295] "CHR_HSCHR7_1_CTG6"
#> [296] "CHR_HSCHR7_1_CTG7"
#> [297] "CHR_HSCHR7_2_CTG1"
#> [298] "CHR_HSCHR7_2_CTG4_4"
#> [299] "CHR_HSCHR7_2_CTG6"
#> [300] "CHR_HSCHR7_2_CTG7"
#> [301] "CHR_HSCHR7_3_CTG6"
#> [302] "CHR_HSCHR8_1_CTG1"
#> [303] "CHR_HSCHR8_1_CTG6"
#> [304] "CHR_HSCHR8_1_CTG7"
#> [305] "CHR_HSCHR8_2_CTG1"
#> [306] "CHR_HSCHR8_2_CTG7"
#> [307] "CHR_HSCHR8_3_CTG1"
#> [308] "CHR_HSCHR8_3_CTG7"
#> [309] "CHR_HSCHR8_4_CTG1"
#> [310] "CHR_HSCHR8_4_CTG7"
#> [311] "CHR_HSCHR8_5_CTG1"
#> [312] "CHR_HSCHR8_5_CTG7"
#> [313] "CHR_HSCHR8_6_CTG1"
#> [314] "CHR_HSCHR8_7_CTG1"
#> [315] "CHR_HSCHR8_8_CTG1"
#> [316] "CHR_HSCHR8_9_CTG1"
#> [317] "CHR_HSCHR9_1_CTG1"
#> [318] "CHR_HSCHR9_1_CTG2"
#> [319] "CHR_HSCHR9_1_CTG3"
#> [320] "CHR_HSCHR9_1_CTG4"
#> [321] "CHR_HSCHR9_1_CTG5"
#> [322] "CHR_HSCHR9_1_CTG6"
#> [323] "CHR_HSCHRX_1_CTG3"
#> [324] "CHR_HSCHRX_2_CTG12"
#> [325] "CHR_HSCHRX_2_CTG3"
#> [326] "GL000009.2"
#> [327] "GL000194.1"
#> [328] "GL000195.1"
#> [329] "GL000205.2"
#> [330] "GL000213.1"
#> [331] "GL000216.2"
#> [332] "GL000218.1"
#> [333] "GL000219.1"
#> [334] "GL000220.1"
#> [335] "GL000225.1"
#> [336] "KI270442.1"
#> [337] "KI270711.1"
#> [338] "KI270713.1"
#> [339] "KI270721.1"
#> [340] "KI270726.1"
#> [341] "KI270727.1"
#> [342] "KI270728.1"
#> [343] "KI270731.1"
#> [344] "KI270733.1"
#> [345] "KI270734.1"
#> [346] "KI270744.1"
#> [347] "KI270750.1"
#> [348] "LRG_183"
#> [349] "LRG_187"
#> [350] "LRG_239"
#> [351] "LRG_311"
#> [352] "LRG_721"
#> [353] "LRG_741"
#> [354] "LRG_93"
#> [355] "MT"
#> [356] "X"
#> [357] "Y"
## Get all supported mappings for the organism of the EnsDb.
supportedSeqlevelsStyles(edb)
#> NULL
## Change the seqlevels to UCSC style.
seqlevelsStyle(edb) <- "UCSC"
seqlevels(edb)
#> Warning: More than 5 seqnames with seqlevels style of the database (Ensembl) could not be mapped to the seqlevels style: UCSC!) Returning the orginal seqnames for these.
#> [1] "chr1"
#> [2] "chr10"
#> [3] "chr11"
#> [4] "chr12"
#> [5] "chr13"
#> [6] "chr14"
#> [7] "chr15"
#> [8] "chr16"
#> [9] "chr17"
#> [10] "chr18"
#> [11] "chr19"
#> [12] "chr2"
#> [13] "chr20"
#> [14] "chr21"
#> [15] "chr22"
#> [16] "chr3"
#> [17] "chr4"
#> [18] "chr5"
#> [19] "chr6"
#> [20] "chr7"
#> [21] "chr8"
#> [22] "chr9"
#> [23] "CHR_HG107_PATCH"
#> [24] "CHR_HG126_PATCH"
#> [25] "CHR_HG1311_PATCH"
#> [26] "CHR_HG1342_HG2282_PATCH"
#> [27] "CHR_HG1362_PATCH"
#> [28] "CHR_HG142_HG150_NOVEL_TEST"
#> [29] "CHR_HG151_NOVEL_TEST"
#> [30] "CHR_HG1651_PATCH"
#> [31] "CHR_HG1832_PATCH"
#> [32] "CHR_HG2021_PATCH"
#> [33] "CHR_HG2022_PATCH"
#> [34] "CHR_HG2023_PATCH"
#> [35] "CHR_HG2030_PATCH"
#> [36] "CHR_HG2058_PATCH"
#> [37] "CHR_HG2062_PATCH"
#> [38] "CHR_HG2063_PATCH"
#> [39] "CHR_HG2066_PATCH"
#> [40] "CHR_HG2072_PATCH"
#> [41] "CHR_HG2095_PATCH"
#> [42] "CHR_HG2104_PATCH"
#> [43] "CHR_HG2116_PATCH"
#> [44] "CHR_HG2128_PATCH"
#> [45] "CHR_HG2191_PATCH"
#> [46] "CHR_HG2213_PATCH"
#> [47] "CHR_HG2217_PATCH"
#> [48] "CHR_HG2232_PATCH"
#> [49] "CHR_HG2233_PATCH"
#> [50] "CHR_HG2235_PATCH"
#> [51] "CHR_HG2239_PATCH"
#> [52] "CHR_HG2247_PATCH"
#> [53] "CHR_HG2249_PATCH"
#> [54] "CHR_HG2288_HG2289_PATCH"
#> [55] "CHR_HG2290_PATCH"
#> [56] "CHR_HG2291_PATCH"
#> [57] "CHR_HG2334_PATCH"
#> [58] "CHR_HG26_PATCH"
#> [59] "CHR_HG986_PATCH"
#> [60] "CHR_HSCHR10_1_CTG1"
#> [61] "CHR_HSCHR10_1_CTG2"
#> [62] "CHR_HSCHR10_1_CTG3"
#> [63] "CHR_HSCHR10_1_CTG4"
#> [64] "CHR_HSCHR10_1_CTG6"
#> [65] "CHR_HSCHR11_1_CTG1_2"
#> [66] "CHR_HSCHR11_1_CTG5"
#> [67] "CHR_HSCHR11_1_CTG6"
#> [68] "CHR_HSCHR11_1_CTG7"
#> [69] "CHR_HSCHR11_1_CTG8"
#> [70] "CHR_HSCHR11_2_CTG1"
#> [71] "CHR_HSCHR11_2_CTG1_1"
#> [72] "CHR_HSCHR11_3_CTG1"
#> [73] "CHR_HSCHR12_1_CTG1"
#> [74] "CHR_HSCHR12_1_CTG2_1"
#> [75] "CHR_HSCHR12_2_CTG1"
#> [76] "CHR_HSCHR12_2_CTG2"
#> [77] "CHR_HSCHR12_2_CTG2_1"
#> [78] "CHR_HSCHR12_3_CTG2"
#> [79] "CHR_HSCHR12_3_CTG2_1"
#> [80] "CHR_HSCHR12_4_CTG2"
#> [81] "CHR_HSCHR12_4_CTG2_1"
#> [82] "CHR_HSCHR12_5_CTG2"
#> [83] "CHR_HSCHR12_5_CTG2_1"
#> [84] "CHR_HSCHR12_6_CTG2_1"
#> [85] "CHR_HSCHR13_1_CTG1"
#> [86] "CHR_HSCHR13_1_CTG3"
#> [87] "CHR_HSCHR13_1_CTG5"
#> [88] "CHR_HSCHR13_1_CTG8"
#> [89] "CHR_HSCHR14_1_CTG1"
#> [90] "CHR_HSCHR14_2_CTG1"
#> [91] "CHR_HSCHR14_3_CTG1"
#> [92] "CHR_HSCHR14_7_CTG1"
#> [93] "CHR_HSCHR15_1_CTG1"
#> [94] "CHR_HSCHR15_1_CTG3"
#> [95] "CHR_HSCHR15_1_CTG8"
#> [96] "CHR_HSCHR15_2_CTG3"
#> [97] "CHR_HSCHR15_2_CTG8"
#> [98] "CHR_HSCHR15_3_CTG3"
#> [99] "CHR_HSCHR15_3_CTG8"
#> [100] "CHR_HSCHR15_4_CTG8"
#> [101] "CHR_HSCHR15_5_CTG8"
#> [102] "CHR_HSCHR15_6_CTG8"
#> [103] "CHR_HSCHR16_1_CTG1"
#> [104] "CHR_HSCHR16_1_CTG3_1"
#> [105] "CHR_HSCHR16_2_CTG3_1"
#> [106] "CHR_HSCHR16_3_CTG1"
#> [107] "CHR_HSCHR16_4_CTG1"
#> [108] "CHR_HSCHR16_4_CTG3_1"
#> [109] "CHR_HSCHR16_5_CTG1"
#> [110] "CHR_HSCHR16_CTG2"
#> [111] "CHR_HSCHR17_10_CTG4"
#> [112] "CHR_HSCHR17_1_CTG1"
#> [113] "CHR_HSCHR17_1_CTG2"
#> [114] "CHR_HSCHR17_1_CTG4"
#> [115] "CHR_HSCHR17_1_CTG5"
#> [116] "CHR_HSCHR17_1_CTG9"
#> [117] "CHR_HSCHR17_2_CTG1"
#> [118] "CHR_HSCHR17_2_CTG2"
#> [119] "CHR_HSCHR17_2_CTG4"
#> [120] "CHR_HSCHR17_2_CTG5"
#> [121] "CHR_HSCHR17_3_CTG2"
#> [122] "CHR_HSCHR17_3_CTG4"
#> [123] "CHR_HSCHR17_4_CTG4"
#> [124] "CHR_HSCHR17_5_CTG4"
#> [125] "CHR_HSCHR17_6_CTG4"
#> [126] "CHR_HSCHR17_7_CTG4"
#> [127] "CHR_HSCHR17_8_CTG4"
#> [128] "CHR_HSCHR17_9_CTG4"
#> [129] "CHR_HSCHR18_1_CTG1_1"
#> [130] "CHR_HSCHR18_1_CTG2_1"
#> [131] "CHR_HSCHR18_2_CTG1_1"
#> [132] "CHR_HSCHR18_2_CTG2"
#> [133] "CHR_HSCHR18_2_CTG2_1"
#> [134] "CHR_HSCHR18_3_CTG2_1"
#> [135] "CHR_HSCHR18_5_CTG1_1"
#> [136] "CHR_HSCHR18_ALT21_CTG2_1"
#> [137] "CHR_HSCHR18_ALT2_CTG2_1"
#> [138] "CHR_HSCHR19KIR_ABC08_A1_HAP_CTG3_1"
#> [139] "CHR_HSCHR19KIR_ABC08_AB_HAP_C_P_CTG3_1"
#> [140] "CHR_HSCHR19KIR_ABC08_AB_HAP_T_P_CTG3_1"
#> [141] "CHR_HSCHR19KIR_FH05_A_HAP_CTG3_1"
#> [142] "CHR_HSCHR19KIR_FH05_B_HAP_CTG3_1"
#> [143] "CHR_HSCHR19KIR_FH06_A_HAP_CTG3_1"
#> [144] "CHR_HSCHR19KIR_FH06_BA1_HAP_CTG3_1"
#> [145] "CHR_HSCHR19KIR_FH08_A_HAP_CTG3_1"
#> [146] "CHR_HSCHR19KIR_FH08_BAX_HAP_CTG3_1"
#> [147] "CHR_HSCHR19KIR_FH13_A_HAP_CTG3_1"
#> [148] "CHR_HSCHR19KIR_FH13_BA2_HAP_CTG3_1"
#> [149] "CHR_HSCHR19KIR_FH15_A_HAP_CTG3_1"
#> [150] "CHR_HSCHR19KIR_FH15_B_HAP_CTG3_1"
#> [151] "CHR_HSCHR19KIR_G085_A_HAP_CTG3_1"
#> [152] "CHR_HSCHR19KIR_G085_BA1_HAP_CTG3_1"
#> [153] "CHR_HSCHR19KIR_G248_A_HAP_CTG3_1"
#> [154] "CHR_HSCHR19KIR_G248_BA2_HAP_CTG3_1"
#> [155] "CHR_HSCHR19KIR_GRC212_AB_HAP_CTG3_1"
#> [156] "CHR_HSCHR19KIR_GRC212_BA1_HAP_CTG3_1"
#> [157] "CHR_HSCHR19KIR_LUCE_A_HAP_CTG3_1"
#> [158] "CHR_HSCHR19KIR_LUCE_BDEL_HAP_CTG3_1"
#> [159] "CHR_HSCHR19KIR_RP5_B_HAP_CTG3_1"
#> [160] "CHR_HSCHR19KIR_RSH_A_HAP_CTG3_1"
#> [161] "CHR_HSCHR19KIR_RSH_BA2_HAP_CTG3_1"
#> [162] "CHR_HSCHR19KIR_T7526_A_HAP_CTG3_1"
#> [163] "CHR_HSCHR19KIR_T7526_BDEL_HAP_CTG3_1"
#> [164] "CHR_HSCHR19LRC_COX1_CTG3_1"
#> [165] "CHR_HSCHR19LRC_COX2_CTG3_1"
#> [166] "CHR_HSCHR19LRC_LRC_I_CTG3_1"
#> [167] "CHR_HSCHR19LRC_LRC_J_CTG3_1"
#> [168] "CHR_HSCHR19LRC_LRC_S_CTG3_1"
#> [169] "CHR_HSCHR19LRC_LRC_T_CTG3_1"
#> [170] "CHR_HSCHR19LRC_PGF1_CTG3_1"
#> [171] "CHR_HSCHR19LRC_PGF2_CTG3_1"
#> [172] "CHR_HSCHR19_1_CTG2"
#> [173] "CHR_HSCHR19_1_CTG3_1"
#> [174] "CHR_HSCHR19_2_CTG2"
#> [175] "CHR_HSCHR19_2_CTG3_1"
#> [176] "CHR_HSCHR19_3_CTG2"
#> [177] "CHR_HSCHR19_3_CTG3_1"
#> [178] "CHR_HSCHR19_4_CTG2"
#> [179] "CHR_HSCHR19_4_CTG3_1"
#> [180] "CHR_HSCHR19_5_CTG2"
#> [181] "CHR_HSCHR1_1_CTG11"
#> [182] "CHR_HSCHR1_1_CTG3"
#> [183] "CHR_HSCHR1_1_CTG31"
#> [184] "CHR_HSCHR1_1_CTG32_1"
#> [185] "CHR_HSCHR1_2_CTG3"
#> [186] "CHR_HSCHR1_2_CTG31"
#> [187] "CHR_HSCHR1_2_CTG32_1"
#> [188] "CHR_HSCHR1_3_CTG3"
#> [189] "CHR_HSCHR1_3_CTG31"
#> [190] "CHR_HSCHR1_3_CTG32_1"
#> [191] "CHR_HSCHR1_4_CTG3"
#> [192] "CHR_HSCHR1_4_CTG31"
#> [193] "CHR_HSCHR1_5_CTG3"
#> [194] "CHR_HSCHR1_5_CTG32_1"
#> [195] "CHR_HSCHR1_ALT2_1_CTG32_1"
#> [196] "CHR_HSCHR20_1_CTG1"
#> [197] "CHR_HSCHR20_1_CTG2"
#> [198] "CHR_HSCHR20_1_CTG3"
#> [199] "CHR_HSCHR20_1_CTG4"
#> [200] "CHR_HSCHR21_2_CTG1_1"
#> [201] "CHR_HSCHR21_3_CTG1_1"
#> [202] "CHR_HSCHR21_4_CTG1_1"
#> [203] "CHR_HSCHR21_5_CTG2"
#> [204] "CHR_HSCHR21_6_CTG1_1"
#> [205] "CHR_HSCHR21_8_CTG1_1"
#> [206] "CHR_HSCHR22_1_CTG1"
#> [207] "CHR_HSCHR22_1_CTG2"
#> [208] "CHR_HSCHR22_1_CTG3"
#> [209] "CHR_HSCHR22_1_CTG4"
#> [210] "CHR_HSCHR22_1_CTG5"
#> [211] "CHR_HSCHR22_1_CTG6"
#> [212] "CHR_HSCHR22_1_CTG7"
#> [213] "CHR_HSCHR22_2_CTG1"
#> [214] "CHR_HSCHR22_3_CTG1"
#> [215] "CHR_HSCHR22_4_CTG1"
#> [216] "CHR_HSCHR22_5_CTG1"
#> [217] "CHR_HSCHR22_6_CTG1"
#> [218] "CHR_HSCHR22_7_CTG1"
#> [219] "CHR_HSCHR22_8_CTG1"
#> [220] "CHR_HSCHR2_1_CTG1"
#> [221] "CHR_HSCHR2_1_CTG15"
#> [222] "CHR_HSCHR2_1_CTG5"
#> [223] "CHR_HSCHR2_1_CTG7"
#> [224] "CHR_HSCHR2_1_CTG7_2"
#> [225] "CHR_HSCHR2_2_CTG1"
#> [226] "CHR_HSCHR2_2_CTG15"
#> [227] "CHR_HSCHR2_2_CTG7"
#> [228] "CHR_HSCHR2_2_CTG7_2"
#> [229] "CHR_HSCHR2_3_CTG1"
#> [230] "CHR_HSCHR2_3_CTG15"
#> [231] "CHR_HSCHR2_3_CTG7_2"
#> [232] "CHR_HSCHR2_4_CTG1"
#> [233] "CHR_HSCHR2_6_CTG7_2"
#> [234] "CHR_HSCHR3_1_CTG1"
#> [235] "CHR_HSCHR3_1_CTG2_1"
#> [236] "CHR_HSCHR3_1_CTG3"
#> [237] "CHR_HSCHR3_2_CTG2_1"
#> [238] "CHR_HSCHR3_2_CTG3"
#> [239] "CHR_HSCHR3_3_CTG1"
#> [240] "CHR_HSCHR3_3_CTG3"
#> [241] "CHR_HSCHR3_4_CTG2_1"
#> [242] "CHR_HSCHR3_4_CTG3"
#> [243] "CHR_HSCHR3_5_CTG2_1"
#> [244] "CHR_HSCHR3_5_CTG3"
#> [245] "CHR_HSCHR3_6_CTG3"
#> [246] "CHR_HSCHR3_7_CTG3"
#> [247] "CHR_HSCHR3_8_CTG3"
#> [248] "CHR_HSCHR3_9_CTG3"
#> [249] "CHR_HSCHR4_11_CTG12"
#> [250] "CHR_HSCHR4_1_CTG12"
#> [251] "CHR_HSCHR4_1_CTG4"
#> [252] "CHR_HSCHR4_1_CTG6"
#> [253] "CHR_HSCHR4_1_CTG9"
#> [254] "CHR_HSCHR4_2_CTG12"
#> [255] "CHR_HSCHR4_2_CTG4"
#> [256] "CHR_HSCHR4_3_CTG12"
#> [257] "CHR_HSCHR4_4_CTG12"
#> [258] "CHR_HSCHR4_5_CTG12"
#> [259] "CHR_HSCHR4_6_CTG12"
#> [260] "CHR_HSCHR4_7_CTG12"
#> [261] "CHR_HSCHR4_8_CTG12"
#> [262] "CHR_HSCHR4_9_CTG12"
#> [263] "CHR_HSCHR5_1_CTG1"
#> [264] "CHR_HSCHR5_1_CTG1_1"
#> [265] "CHR_HSCHR5_1_CTG5"
#> [266] "CHR_HSCHR5_2_CTG1"
#> [267] "CHR_HSCHR5_2_CTG1_1"
#> [268] "CHR_HSCHR5_2_CTG5"
#> [269] "CHR_HSCHR5_3_CTG1"
#> [270] "CHR_HSCHR5_3_CTG5"
#> [271] "CHR_HSCHR5_4_CTG1"
#> [272] "CHR_HSCHR5_4_CTG1_1"
#> [273] "CHR_HSCHR5_5_CTG1"
#> [274] "CHR_HSCHR5_6_CTG1"
#> [275] "CHR_HSCHR5_7_CTG1"
#> [276] "CHR_HSCHR6_1_CTG10"
#> [277] "CHR_HSCHR6_1_CTG2"
#> [278] "CHR_HSCHR6_1_CTG3"
#> [279] "CHR_HSCHR6_1_CTG4"
#> [280] "CHR_HSCHR6_1_CTG5"
#> [281] "CHR_HSCHR6_1_CTG6"
#> [282] "CHR_HSCHR6_1_CTG7"
#> [283] "CHR_HSCHR6_1_CTG8"
#> [284] "CHR_HSCHR6_1_CTG9"
#> [285] "CHR_HSCHR6_8_CTG1"
#> [286] "CHR_HSCHR6_MHC_APD_CTG1"
#> [287] "CHR_HSCHR6_MHC_COX_CTG1"
#> [288] "CHR_HSCHR6_MHC_DBB_CTG1"
#> [289] "CHR_HSCHR6_MHC_MANN_CTG1"
#> [290] "CHR_HSCHR6_MHC_MCF_CTG1"
#> [291] "CHR_HSCHR6_MHC_QBL_CTG1"
#> [292] "CHR_HSCHR6_MHC_SSTO_CTG1"
#> [293] "CHR_HSCHR7_1_CTG1"
#> [294] "CHR_HSCHR7_1_CTG4_4"
#> [295] "CHR_HSCHR7_1_CTG6"
#> [296] "CHR_HSCHR7_1_CTG7"
#> [297] "CHR_HSCHR7_2_CTG1"
#> [298] "CHR_HSCHR7_2_CTG4_4"
#> [299] "CHR_HSCHR7_2_CTG6"
#> [300] "CHR_HSCHR7_2_CTG7"
#> [301] "CHR_HSCHR7_3_CTG6"
#> [302] "CHR_HSCHR8_1_CTG1"
#> [303] "CHR_HSCHR8_1_CTG6"
#> [304] "CHR_HSCHR8_1_CTG7"
#> [305] "CHR_HSCHR8_2_CTG1"
#> [306] "CHR_HSCHR8_2_CTG7"
#> [307] "CHR_HSCHR8_3_CTG1"
#> [308] "CHR_HSCHR8_3_CTG7"
#> [309] "CHR_HSCHR8_4_CTG1"
#> [310] "CHR_HSCHR8_4_CTG7"
#> [311] "CHR_HSCHR8_5_CTG1"
#> [312] "CHR_HSCHR8_5_CTG7"
#> [313] "CHR_HSCHR8_6_CTG1"
#> [314] "CHR_HSCHR8_7_CTG1"
#> [315] "CHR_HSCHR8_8_CTG1"
#> [316] "CHR_HSCHR8_9_CTG1"
#> [317] "CHR_HSCHR9_1_CTG1"
#> [318] "CHR_HSCHR9_1_CTG2"
#> [319] "CHR_HSCHR9_1_CTG3"
#> [320] "CHR_HSCHR9_1_CTG4"
#> [321] "CHR_HSCHR9_1_CTG5"
#> [322] "CHR_HSCHR9_1_CTG6"
#> [323] "CHR_HSCHRX_1_CTG3"
#> [324] "CHR_HSCHRX_2_CTG12"
#> [325] "CHR_HSCHRX_2_CTG3"
#> [326] "GL000009.2"
#> [327] "GL000194.1"
#> [328] "GL000195.1"
#> [329] "GL000205.2"
#> [330] "GL000213.1"
#> [331] "GL000216.2"
#> [332] "GL000218.1"
#> [333] "GL000219.1"
#> [334] "GL000220.1"
#> [335] "GL000225.1"
#> [336] "KI270442.1"
#> [337] "KI270711.1"
#> [338] "KI270713.1"
#> [339] "KI270721.1"
#> [340] "KI270726.1"
#> [341] "KI270727.1"
#> [342] "KI270728.1"
#> [343] "KI270731.1"
#> [344] "KI270733.1"
#> [345] "KI270734.1"
#> [346] "KI270744.1"
#> [347] "KI270750.1"
#> [348] "LRG_183"
#> [349] "LRG_187"
#> [350] "LRG_239"
#> [351] "LRG_311"
#> [352] "LRG_721"
#> [353] "LRG_741"
#> [354] "LRG_93"
#> [355] "chrM"
#> [356] "chrX"
#> [357] "chrY"
## Change the option ensembldb.seqnameNotFound to return NA in case
## the seqname can not be mapped form Ensembl to UCSC.
options(ensembldb.seqnameNotFound = NA)
seqlevels(edb)
#> Warning: More than 5 seqnames with seqlevels style of the database (Ensembl) could not be mapped to the seqlevels style: UCSC!) Returning NA for these.
#> [1] "chr1" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17"
#> [10] "chr18" "chr19" "chr2" "chr20" "chr21" "chr22" "chr3" "chr4" "chr5"
#> [19] "chr6" "chr7" "chr8" "chr9" NA NA NA NA NA
#> [28] NA NA NA NA NA NA NA NA NA
#> [37] NA NA NA NA NA NA NA NA NA
#> [46] NA NA NA NA NA NA NA NA NA
#> [55] NA NA NA NA NA NA NA NA NA
#> [64] NA NA NA NA NA NA NA NA NA
#> [73] NA NA NA NA NA NA NA NA NA
#> [82] NA NA NA NA NA NA NA NA NA
#> [91] NA NA NA NA NA NA NA NA NA
#> [100] NA NA NA NA NA NA NA NA NA
#> [109] NA NA NA NA NA NA NA NA NA
#> [118] NA NA NA NA NA NA NA NA NA
#> [127] NA NA NA NA NA NA NA NA NA
#> [136] NA NA NA NA NA NA NA NA NA
#> [145] NA NA NA NA NA NA NA NA NA
#> [154] NA NA NA NA NA NA NA NA NA
#> [163] NA NA NA NA NA NA NA NA NA
#> [172] NA NA NA NA NA NA NA NA NA
#> [181] NA NA NA NA NA NA NA NA NA
#> [190] NA NA NA NA NA NA NA NA NA
#> [199] NA NA NA NA NA NA NA NA NA
#> [208] NA NA NA NA NA NA NA NA NA
#> [217] NA NA NA NA NA NA NA NA NA
#> [226] NA NA NA NA NA NA NA NA NA
#> [235] NA NA NA NA NA NA NA NA NA
#> [244] NA NA NA NA NA NA NA NA NA
#> [253] NA NA NA NA NA NA NA NA NA
#> [262] NA NA NA NA NA NA NA NA NA
#> [271] NA NA NA NA NA NA NA NA NA
#> [280] NA NA NA NA NA NA NA NA NA
#> [289] NA NA NA NA NA NA NA NA NA
#> [298] NA NA NA NA NA NA NA NA NA
#> [307] NA NA NA NA NA NA NA NA NA
#> [316] NA NA NA NA NA NA NA NA NA
#> [325] NA NA NA NA NA NA NA NA NA
#> [334] NA NA NA NA NA NA NA NA NA
#> [343] NA NA NA NA NA NA NA NA NA
#> [352] NA NA NA "chrM" "chrX" "chrY"
## Defining custom mapping for chromosome names. The `data.frame` should have
## one column named `"Ensembl"` with the original name and an additional column
## with the new names
mymap <- data.frame(Ensembl = c(4, 7, 9, 10),
myway = c("a", "b", "c", "d"))
seqlevelsStyle(edb) <- mymap
seqlevels(edb)
#> Warning: More than 5 seqnames with seqlevels style of the database (Ensembl) could not be mapped to the seqlevels style: myway!) Returning NA for these.
#> [1] NA "d" NA NA NA NA NA NA NA NA NA NA NA NA NA NA "a" NA
#> [19] NA "b" NA "c" NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [37] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [55] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [73] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [91] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [109] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [127] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [145] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [163] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [181] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [199] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [217] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [235] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [253] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [271] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [289] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [307] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [325] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [343] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## This allows us also to rename individual chromosomes but keeping all
## original names for the others.
options(ensembldb.seqnameNotFound = "ORIGINAL")
seqlevels(edb)
#> Warning: More than 5 seqnames with seqlevels style of the database (Ensembl) could not be mapped to the seqlevels style: myway!) Returning the orginal seqnames for these.
#> [1] "1"
#> [2] "d"
#> [3] "11"
#> [4] "12"
#> [5] "13"
#> [6] "14"
#> [7] "15"
#> [8] "16"
#> [9] "17"
#> [10] "18"
#> [11] "19"
#> [12] "2"
#> [13] "20"
#> [14] "21"
#> [15] "22"
#> [16] "3"
#> [17] "a"
#> [18] "5"
#> [19] "6"
#> [20] "b"
#> [21] "8"
#> [22] "c"
#> [23] "CHR_HG107_PATCH"
#> [24] "CHR_HG126_PATCH"
#> [25] "CHR_HG1311_PATCH"
#> [26] "CHR_HG1342_HG2282_PATCH"
#> [27] "CHR_HG1362_PATCH"
#> [28] "CHR_HG142_HG150_NOVEL_TEST"
#> [29] "CHR_HG151_NOVEL_TEST"
#> [30] "CHR_HG1651_PATCH"
#> [31] "CHR_HG1832_PATCH"
#> [32] "CHR_HG2021_PATCH"
#> [33] "CHR_HG2022_PATCH"
#> [34] "CHR_HG2023_PATCH"
#> [35] "CHR_HG2030_PATCH"
#> [36] "CHR_HG2058_PATCH"
#> [37] "CHR_HG2062_PATCH"
#> [38] "CHR_HG2063_PATCH"
#> [39] "CHR_HG2066_PATCH"
#> [40] "CHR_HG2072_PATCH"
#> [41] "CHR_HG2095_PATCH"
#> [42] "CHR_HG2104_PATCH"
#> [43] "CHR_HG2116_PATCH"
#> [44] "CHR_HG2128_PATCH"
#> [45] "CHR_HG2191_PATCH"
#> [46] "CHR_HG2213_PATCH"
#> [47] "CHR_HG2217_PATCH"
#> [48] "CHR_HG2232_PATCH"
#> [49] "CHR_HG2233_PATCH"
#> [50] "CHR_HG2235_PATCH"
#> [51] "CHR_HG2239_PATCH"
#> [52] "CHR_HG2247_PATCH"
#> [53] "CHR_HG2249_PATCH"
#> [54] "CHR_HG2288_HG2289_PATCH"
#> [55] "CHR_HG2290_PATCH"
#> [56] "CHR_HG2291_PATCH"
#> [57] "CHR_HG2334_PATCH"
#> [58] "CHR_HG26_PATCH"
#> [59] "CHR_HG986_PATCH"
#> [60] "CHR_HSCHR10_1_CTG1"
#> [61] "CHR_HSCHR10_1_CTG2"
#> [62] "CHR_HSCHR10_1_CTG3"
#> [63] "CHR_HSCHR10_1_CTG4"
#> [64] "CHR_HSCHR10_1_CTG6"
#> [65] "CHR_HSCHR11_1_CTG1_2"
#> [66] "CHR_HSCHR11_1_CTG5"
#> [67] "CHR_HSCHR11_1_CTG6"
#> [68] "CHR_HSCHR11_1_CTG7"
#> [69] "CHR_HSCHR11_1_CTG8"
#> [70] "CHR_HSCHR11_2_CTG1"
#> [71] "CHR_HSCHR11_2_CTG1_1"
#> [72] "CHR_HSCHR11_3_CTG1"
#> [73] "CHR_HSCHR12_1_CTG1"
#> [74] "CHR_HSCHR12_1_CTG2_1"
#> [75] "CHR_HSCHR12_2_CTG1"
#> [76] "CHR_HSCHR12_2_CTG2"
#> [77] "CHR_HSCHR12_2_CTG2_1"
#> [78] "CHR_HSCHR12_3_CTG2"
#> [79] "CHR_HSCHR12_3_CTG2_1"
#> [80] "CHR_HSCHR12_4_CTG2"
#> [81] "CHR_HSCHR12_4_CTG2_1"
#> [82] "CHR_HSCHR12_5_CTG2"
#> [83] "CHR_HSCHR12_5_CTG2_1"
#> [84] "CHR_HSCHR12_6_CTG2_1"
#> [85] "CHR_HSCHR13_1_CTG1"
#> [86] "CHR_HSCHR13_1_CTG3"
#> [87] "CHR_HSCHR13_1_CTG5"
#> [88] "CHR_HSCHR13_1_CTG8"
#> [89] "CHR_HSCHR14_1_CTG1"
#> [90] "CHR_HSCHR14_2_CTG1"
#> [91] "CHR_HSCHR14_3_CTG1"
#> [92] "CHR_HSCHR14_7_CTG1"
#> [93] "CHR_HSCHR15_1_CTG1"
#> [94] "CHR_HSCHR15_1_CTG3"
#> [95] "CHR_HSCHR15_1_CTG8"
#> [96] "CHR_HSCHR15_2_CTG3"
#> [97] "CHR_HSCHR15_2_CTG8"
#> [98] "CHR_HSCHR15_3_CTG3"
#> [99] "CHR_HSCHR15_3_CTG8"
#> [100] "CHR_HSCHR15_4_CTG8"
#> [101] "CHR_HSCHR15_5_CTG8"
#> [102] "CHR_HSCHR15_6_CTG8"
#> [103] "CHR_HSCHR16_1_CTG1"
#> [104] "CHR_HSCHR16_1_CTG3_1"
#> [105] "CHR_HSCHR16_2_CTG3_1"
#> [106] "CHR_HSCHR16_3_CTG1"
#> [107] "CHR_HSCHR16_4_CTG1"
#> [108] "CHR_HSCHR16_4_CTG3_1"
#> [109] "CHR_HSCHR16_5_CTG1"
#> [110] "CHR_HSCHR16_CTG2"
#> [111] "CHR_HSCHR17_10_CTG4"
#> [112] "CHR_HSCHR17_1_CTG1"
#> [113] "CHR_HSCHR17_1_CTG2"
#> [114] "CHR_HSCHR17_1_CTG4"
#> [115] "CHR_HSCHR17_1_CTG5"
#> [116] "CHR_HSCHR17_1_CTG9"
#> [117] "CHR_HSCHR17_2_CTG1"
#> [118] "CHR_HSCHR17_2_CTG2"
#> [119] "CHR_HSCHR17_2_CTG4"
#> [120] "CHR_HSCHR17_2_CTG5"
#> [121] "CHR_HSCHR17_3_CTG2"
#> [122] "CHR_HSCHR17_3_CTG4"
#> [123] "CHR_HSCHR17_4_CTG4"
#> [124] "CHR_HSCHR17_5_CTG4"
#> [125] "CHR_HSCHR17_6_CTG4"
#> [126] "CHR_HSCHR17_7_CTG4"
#> [127] "CHR_HSCHR17_8_CTG4"
#> [128] "CHR_HSCHR17_9_CTG4"
#> [129] "CHR_HSCHR18_1_CTG1_1"
#> [130] "CHR_HSCHR18_1_CTG2_1"
#> [131] "CHR_HSCHR18_2_CTG1_1"
#> [132] "CHR_HSCHR18_2_CTG2"
#> [133] "CHR_HSCHR18_2_CTG2_1"
#> [134] "CHR_HSCHR18_3_CTG2_1"
#> [135] "CHR_HSCHR18_5_CTG1_1"
#> [136] "CHR_HSCHR18_ALT21_CTG2_1"
#> [137] "CHR_HSCHR18_ALT2_CTG2_1"
#> [138] "CHR_HSCHR19KIR_ABC08_A1_HAP_CTG3_1"
#> [139] "CHR_HSCHR19KIR_ABC08_AB_HAP_C_P_CTG3_1"
#> [140] "CHR_HSCHR19KIR_ABC08_AB_HAP_T_P_CTG3_1"
#> [141] "CHR_HSCHR19KIR_FH05_A_HAP_CTG3_1"
#> [142] "CHR_HSCHR19KIR_FH05_B_HAP_CTG3_1"
#> [143] "CHR_HSCHR19KIR_FH06_A_HAP_CTG3_1"
#> [144] "CHR_HSCHR19KIR_FH06_BA1_HAP_CTG3_1"
#> [145] "CHR_HSCHR19KIR_FH08_A_HAP_CTG3_1"
#> [146] "CHR_HSCHR19KIR_FH08_BAX_HAP_CTG3_1"
#> [147] "CHR_HSCHR19KIR_FH13_A_HAP_CTG3_1"
#> [148] "CHR_HSCHR19KIR_FH13_BA2_HAP_CTG3_1"
#> [149] "CHR_HSCHR19KIR_FH15_A_HAP_CTG3_1"
#> [150] "CHR_HSCHR19KIR_FH15_B_HAP_CTG3_1"
#> [151] "CHR_HSCHR19KIR_G085_A_HAP_CTG3_1"
#> [152] "CHR_HSCHR19KIR_G085_BA1_HAP_CTG3_1"
#> [153] "CHR_HSCHR19KIR_G248_A_HAP_CTG3_1"
#> [154] "CHR_HSCHR19KIR_G248_BA2_HAP_CTG3_1"
#> [155] "CHR_HSCHR19KIR_GRC212_AB_HAP_CTG3_1"
#> [156] "CHR_HSCHR19KIR_GRC212_BA1_HAP_CTG3_1"
#> [157] "CHR_HSCHR19KIR_LUCE_A_HAP_CTG3_1"
#> [158] "CHR_HSCHR19KIR_LUCE_BDEL_HAP_CTG3_1"
#> [159] "CHR_HSCHR19KIR_RP5_B_HAP_CTG3_1"
#> [160] "CHR_HSCHR19KIR_RSH_A_HAP_CTG3_1"
#> [161] "CHR_HSCHR19KIR_RSH_BA2_HAP_CTG3_1"
#> [162] "CHR_HSCHR19KIR_T7526_A_HAP_CTG3_1"
#> [163] "CHR_HSCHR19KIR_T7526_BDEL_HAP_CTG3_1"
#> [164] "CHR_HSCHR19LRC_COX1_CTG3_1"
#> [165] "CHR_HSCHR19LRC_COX2_CTG3_1"
#> [166] "CHR_HSCHR19LRC_LRC_I_CTG3_1"
#> [167] "CHR_HSCHR19LRC_LRC_J_CTG3_1"
#> [168] "CHR_HSCHR19LRC_LRC_S_CTG3_1"
#> [169] "CHR_HSCHR19LRC_LRC_T_CTG3_1"
#> [170] "CHR_HSCHR19LRC_PGF1_CTG3_1"
#> [171] "CHR_HSCHR19LRC_PGF2_CTG3_1"
#> [172] "CHR_HSCHR19_1_CTG2"
#> [173] "CHR_HSCHR19_1_CTG3_1"
#> [174] "CHR_HSCHR19_2_CTG2"
#> [175] "CHR_HSCHR19_2_CTG3_1"
#> [176] "CHR_HSCHR19_3_CTG2"
#> [177] "CHR_HSCHR19_3_CTG3_1"
#> [178] "CHR_HSCHR19_4_CTG2"
#> [179] "CHR_HSCHR19_4_CTG3_1"
#> [180] "CHR_HSCHR19_5_CTG2"
#> [181] "CHR_HSCHR1_1_CTG11"
#> [182] "CHR_HSCHR1_1_CTG3"
#> [183] "CHR_HSCHR1_1_CTG31"
#> [184] "CHR_HSCHR1_1_CTG32_1"
#> [185] "CHR_HSCHR1_2_CTG3"
#> [186] "CHR_HSCHR1_2_CTG31"
#> [187] "CHR_HSCHR1_2_CTG32_1"
#> [188] "CHR_HSCHR1_3_CTG3"
#> [189] "CHR_HSCHR1_3_CTG31"
#> [190] "CHR_HSCHR1_3_CTG32_1"
#> [191] "CHR_HSCHR1_4_CTG3"
#> [192] "CHR_HSCHR1_4_CTG31"
#> [193] "CHR_HSCHR1_5_CTG3"
#> [194] "CHR_HSCHR1_5_CTG32_1"
#> [195] "CHR_HSCHR1_ALT2_1_CTG32_1"
#> [196] "CHR_HSCHR20_1_CTG1"
#> [197] "CHR_HSCHR20_1_CTG2"
#> [198] "CHR_HSCHR20_1_CTG3"
#> [199] "CHR_HSCHR20_1_CTG4"
#> [200] "CHR_HSCHR21_2_CTG1_1"
#> [201] "CHR_HSCHR21_3_CTG1_1"
#> [202] "CHR_HSCHR21_4_CTG1_1"
#> [203] "CHR_HSCHR21_5_CTG2"
#> [204] "CHR_HSCHR21_6_CTG1_1"
#> [205] "CHR_HSCHR21_8_CTG1_1"
#> [206] "CHR_HSCHR22_1_CTG1"
#> [207] "CHR_HSCHR22_1_CTG2"
#> [208] "CHR_HSCHR22_1_CTG3"
#> [209] "CHR_HSCHR22_1_CTG4"
#> [210] "CHR_HSCHR22_1_CTG5"
#> [211] "CHR_HSCHR22_1_CTG6"
#> [212] "CHR_HSCHR22_1_CTG7"
#> [213] "CHR_HSCHR22_2_CTG1"
#> [214] "CHR_HSCHR22_3_CTG1"
#> [215] "CHR_HSCHR22_4_CTG1"
#> [216] "CHR_HSCHR22_5_CTG1"
#> [217] "CHR_HSCHR22_6_CTG1"
#> [218] "CHR_HSCHR22_7_CTG1"
#> [219] "CHR_HSCHR22_8_CTG1"
#> [220] "CHR_HSCHR2_1_CTG1"
#> [221] "CHR_HSCHR2_1_CTG15"
#> [222] "CHR_HSCHR2_1_CTG5"
#> [223] "CHR_HSCHR2_1_CTG7"
#> [224] "CHR_HSCHR2_1_CTG7_2"
#> [225] "CHR_HSCHR2_2_CTG1"
#> [226] "CHR_HSCHR2_2_CTG15"
#> [227] "CHR_HSCHR2_2_CTG7"
#> [228] "CHR_HSCHR2_2_CTG7_2"
#> [229] "CHR_HSCHR2_3_CTG1"
#> [230] "CHR_HSCHR2_3_CTG15"
#> [231] "CHR_HSCHR2_3_CTG7_2"
#> [232] "CHR_HSCHR2_4_CTG1"
#> [233] "CHR_HSCHR2_6_CTG7_2"
#> [234] "CHR_HSCHR3_1_CTG1"
#> [235] "CHR_HSCHR3_1_CTG2_1"
#> [236] "CHR_HSCHR3_1_CTG3"
#> [237] "CHR_HSCHR3_2_CTG2_1"
#> [238] "CHR_HSCHR3_2_CTG3"
#> [239] "CHR_HSCHR3_3_CTG1"
#> [240] "CHR_HSCHR3_3_CTG3"
#> [241] "CHR_HSCHR3_4_CTG2_1"
#> [242] "CHR_HSCHR3_4_CTG3"
#> [243] "CHR_HSCHR3_5_CTG2_1"
#> [244] "CHR_HSCHR3_5_CTG3"
#> [245] "CHR_HSCHR3_6_CTG3"
#> [246] "CHR_HSCHR3_7_CTG3"
#> [247] "CHR_HSCHR3_8_CTG3"
#> [248] "CHR_HSCHR3_9_CTG3"
#> [249] "CHR_HSCHR4_11_CTG12"
#> [250] "CHR_HSCHR4_1_CTG12"
#> [251] "CHR_HSCHR4_1_CTG4"
#> [252] "CHR_HSCHR4_1_CTG6"
#> [253] "CHR_HSCHR4_1_CTG9"
#> [254] "CHR_HSCHR4_2_CTG12"
#> [255] "CHR_HSCHR4_2_CTG4"
#> [256] "CHR_HSCHR4_3_CTG12"
#> [257] "CHR_HSCHR4_4_CTG12"
#> [258] "CHR_HSCHR4_5_CTG12"
#> [259] "CHR_HSCHR4_6_CTG12"
#> [260] "CHR_HSCHR4_7_CTG12"
#> [261] "CHR_HSCHR4_8_CTG12"
#> [262] "CHR_HSCHR4_9_CTG12"
#> [263] "CHR_HSCHR5_1_CTG1"
#> [264] "CHR_HSCHR5_1_CTG1_1"
#> [265] "CHR_HSCHR5_1_CTG5"
#> [266] "CHR_HSCHR5_2_CTG1"
#> [267] "CHR_HSCHR5_2_CTG1_1"
#> [268] "CHR_HSCHR5_2_CTG5"
#> [269] "CHR_HSCHR5_3_CTG1"
#> [270] "CHR_HSCHR5_3_CTG5"
#> [271] "CHR_HSCHR5_4_CTG1"
#> [272] "CHR_HSCHR5_4_CTG1_1"
#> [273] "CHR_HSCHR5_5_CTG1"
#> [274] "CHR_HSCHR5_6_CTG1"
#> [275] "CHR_HSCHR5_7_CTG1"
#> [276] "CHR_HSCHR6_1_CTG10"
#> [277] "CHR_HSCHR6_1_CTG2"
#> [278] "CHR_HSCHR6_1_CTG3"
#> [279] "CHR_HSCHR6_1_CTG4"
#> [280] "CHR_HSCHR6_1_CTG5"
#> [281] "CHR_HSCHR6_1_CTG6"
#> [282] "CHR_HSCHR6_1_CTG7"
#> [283] "CHR_HSCHR6_1_CTG8"
#> [284] "CHR_HSCHR6_1_CTG9"
#> [285] "CHR_HSCHR6_8_CTG1"
#> [286] "CHR_HSCHR6_MHC_APD_CTG1"
#> [287] "CHR_HSCHR6_MHC_COX_CTG1"
#> [288] "CHR_HSCHR6_MHC_DBB_CTG1"
#> [289] "CHR_HSCHR6_MHC_MANN_CTG1"
#> [290] "CHR_HSCHR6_MHC_MCF_CTG1"
#> [291] "CHR_HSCHR6_MHC_QBL_CTG1"
#> [292] "CHR_HSCHR6_MHC_SSTO_CTG1"
#> [293] "CHR_HSCHR7_1_CTG1"
#> [294] "CHR_HSCHR7_1_CTG4_4"
#> [295] "CHR_HSCHR7_1_CTG6"
#> [296] "CHR_HSCHR7_1_CTG7"
#> [297] "CHR_HSCHR7_2_CTG1"
#> [298] "CHR_HSCHR7_2_CTG4_4"
#> [299] "CHR_HSCHR7_2_CTG6"
#> [300] "CHR_HSCHR7_2_CTG7"
#> [301] "CHR_HSCHR7_3_CTG6"
#> [302] "CHR_HSCHR8_1_CTG1"
#> [303] "CHR_HSCHR8_1_CTG6"
#> [304] "CHR_HSCHR8_1_CTG7"
#> [305] "CHR_HSCHR8_2_CTG1"
#> [306] "CHR_HSCHR8_2_CTG7"
#> [307] "CHR_HSCHR8_3_CTG1"
#> [308] "CHR_HSCHR8_3_CTG7"
#> [309] "CHR_HSCHR8_4_CTG1"
#> [310] "CHR_HSCHR8_4_CTG7"
#> [311] "CHR_HSCHR8_5_CTG1"
#> [312] "CHR_HSCHR8_5_CTG7"
#> [313] "CHR_HSCHR8_6_CTG1"
#> [314] "CHR_HSCHR8_7_CTG1"
#> [315] "CHR_HSCHR8_8_CTG1"
#> [316] "CHR_HSCHR8_9_CTG1"
#> [317] "CHR_HSCHR9_1_CTG1"
#> [318] "CHR_HSCHR9_1_CTG2"
#> [319] "CHR_HSCHR9_1_CTG3"
#> [320] "CHR_HSCHR9_1_CTG4"
#> [321] "CHR_HSCHR9_1_CTG5"
#> [322] "CHR_HSCHR9_1_CTG6"
#> [323] "CHR_HSCHRX_1_CTG3"
#> [324] "CHR_HSCHRX_2_CTG12"
#> [325] "CHR_HSCHRX_2_CTG3"
#> [326] "GL000009.2"
#> [327] "GL000194.1"
#> [328] "GL000195.1"
#> [329] "GL000205.2"
#> [330] "GL000213.1"
#> [331] "GL000216.2"
#> [332] "GL000218.1"
#> [333] "GL000219.1"
#> [334] "GL000220.1"
#> [335] "GL000225.1"
#> [336] "KI270442.1"
#> [337] "KI270711.1"
#> [338] "KI270713.1"
#> [339] "KI270721.1"
#> [340] "KI270726.1"
#> [341] "KI270727.1"
#> [342] "KI270728.1"
#> [343] "KI270731.1"
#> [344] "KI270733.1"
#> [345] "KI270734.1"
#> [346] "KI270744.1"
#> [347] "KI270750.1"
#> [348] "LRG_183"
#> [349] "LRG_187"
#> [350] "LRG_239"
#> [351] "LRG_311"
#> [352] "LRG_721"
#> [353] "LRG_741"
#> [354] "LRG_93"
#> [355] "MT"
#> [356] "X"
#> [357] "Y"