Name or rename a list of gene trees or gene matrices genes. For internal use mostly.
Arguments
- X
A list of trees or matrices
- gene.names
List of names to assign to the elements of X. Must be of the same length as length(X). If NULL (the default) the object are numbered 1,2,...,length(X).
Examples
data(carnivora)
# names before renaming
names(carnivora)
#> [1] "ENSG00000004478_FKBP4" "ENSG00000005381_MPO"
#> [3] "ENSG00000007944_MYLIP" "ENSG00000012963_UBR7"
#> [5] "ENSG00000022355_GABRA1" "ENSG00000023909_GCLM"
#> [7] "ENSG00000036473_OTC" "ENSG00000048140_TSPAN17"
#> [9] "ENSG00000049449_RCN1" "ENSG00000051620_HEBP2"
#> [11] "ENSG00000054796_SPO11" "ENSG00000069943_PIGB"
#> [13] "ENSG00000070010_UFD1" "ENSG00000072954_TMEM38A"
#> [15] "ENSG00000073111_MCM2" "ENSG00000075336_TIMM21"
#> [17] "ENSG00000075975_MKRN2" "ENSG00000079689_SCGN"
#> [19] "ENSG00000090432_MUL1" "ENSG00000092010_PSME1"
#> [21] "ENSG00000092067_CEBPE" "ENSG00000095380_NANS"
#> [23] "ENSG00000100078_PLA2G3" "ENSG00000100591_AHSA1"
#> [25] "ENSG00000100604_CHGA" "ENSG00000100625_SIX4"
#> [27] "ENSG00000102003_SYP" "ENSG00000102245_CD40LG"
#> [29] "ENSG00000102543_CDADC1" "ENSG00000104147_OIP5"
#> [31] "ENSG00000104221_BRF2" "ENSG00000104679_R3HCC1"
#> [33] "ENSG00000105141_CASP14" "ENSG00000105197_TIMM50"
#> [35] "ENSG00000105254_TBCB" "ENSG00000105258_POLR2I"
#> [37] "ENSG00000106128_GHRHR" "ENSG00000106511_MEOX2"
#> [39] "ENSG00000107815_TWNK" "ENSG00000109072_VTN"
#> [41] "ENSG00000109471_IL2" "ENSG00000110057_UNC93B1"
#> [43] "ENSG00000110811_P3H3" "ENSG00000110944_IL23A"
#> [45] "ENSG00000112096_SOD2" "ENSG00000113302_IL12B"
#> [47] "ENSG00000113555_PCDH12" "ENSG00000113734_BNIP1"
#> [49] "ENSG00000114388_NPRL2" "ENSG00000114491_UMPS"
#> [51] "ENSG00000114638_UPK1B" "ENSG00000114686_MRPL3"
#> [53] "ENSG00000114779_ABHD14B" "ENSG00000115665_SLC5A7"
#> [55] "ENSG00000116157_GPX7" "ENSG00000116761_CTH"
#> [57] "ENSG00000117600_PLPPR4" "ENSG00000118271_TTR"
#> [59] "ENSG00000119396_RAB14" "ENSG00000120053_GOT1"
#> [61] "ENSG00000120659_TNFSF11" "ENSG00000121073_SLC35B1"
#> [63] "ENSG00000121900_TMEM54" "ENSG00000123307_NEUROD4"
#> [65] "ENSG00000123999_INHA" "ENSG00000124357_NAGK"
#> [67] "ENSG00000125538_IL1B" "ENSG00000126353_CCR7"
#> [69] "ENSG00000127337_YEATS4" "ENSG00000127993_RBM48"
#> [71] "ENSG00000128463_EMC4" "ENSG00000128886_ELL3"
#> [73] "ENSG00000128965_CHAC1" "ENSG00000130766_SESN2"
#> [75] "ENSG00000131013_PPIL4" "ENSG00000132254_ARFIP2"
#> [77] "ENSG00000132275_RRP8" "ENSG00000132463_GRSF1"
#> [79] "ENSG00000132693_CRP" "ENSG00000133065_SLC41A1"
#> [81] "ENSG00000133135_RNF128" "ENSG00000133318_RTN3"
#> [83] "ENSG00000134107_BHLHE40" "ENSG00000134240_HMGCS2"
#> [85] "ENSG00000134588_USP26" "ENSG00000134901_KDELC1"
#> [87] "ENSG00000135452_TSPAN31" "ENSG00000135469_COQ10A"
#> [89] "ENSG00000136156_ITM2B" "ENSG00000136634_IL10"
#> [91] "ENSG00000136807_CDK9" "ENSG00000136932_TRMO"
#> [93] "ENSG00000136999_NOV" "ENSG00000138231_DBR1"
#> [95] "ENSG00000138675_FGF5" "ENSG00000139572_GPR84"
#> [97] "ENSG00000140274_DUOXA2" "ENSG00000140450_ARRDC4"
#> [99] "ENSG00000140459_CYP11A1" "ENSG00000141200_KIF2B"
#> [101] "ENSG00000141349_G6PC3" "ENSG00000141753_IGFBP4"
#> [103] "ENSG00000142039_CCDC97" "ENSG00000142733_MAP3K6"
#> [105] "ENSG00000142871_CYR61" "ENSG00000143125_PROK1"
#> [107] "ENSG00000143153_ATP1B1" "ENSG00000143196_DPT"
#> [109] "ENSG00000143942_CHAC2" "ENSG00000144136_SLC20A1"
#> [111] "ENSG00000144355_DLX1" "ENSG00000145050_MANF"
#> [113] "ENSG00000145384_FABP2" "ENSG00000145391_SETD7"
#> [115] "ENSG00000145649_GZMA" "ENSG00000147457_CHMP7"
#> [117] "ENSG00000147679_UTP23" "ENSG00000148229_POLE3"
#> [119] "ENSG00000148331_ASB6" "ENSG00000148334_PTGES2"
#> [121] "ENSG00000148677_ANKRD1" "ENSG00000148795_CYP17A1"
#> [123] "ENSG00000149243_KLHL35" "ENSG00000149573_MPZL2"
#> [125] "ENSG00000151611_MMAA"
carnivora.renamed<-rename.genes(carnivora, gene.names=as.character(1:length(carnivora)))
# names after renaming
names(carnivora.renamed)
#> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12"
#> [13] "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24"
#> [25] "25" "26" "27" "28" "29" "30" "31" "32" "33" "34" "35" "36"
#> [37] "37" "38" "39" "40" "41" "42" "43" "44" "45" "46" "47" "48"
#> [49] "49" "50" "51" "52" "53" "54" "55" "56" "57" "58" "59" "60"
#> [61] "61" "62" "63" "64" "65" "66" "67" "68" "69" "70" "71" "72"
#> [73] "73" "74" "75" "76" "77" "78" "79" "80" "81" "82" "83" "84"
#> [85] "85" "86" "87" "88" "89" "90" "91" "92" "93" "94" "95" "96"
#> [97] "97" "98" "99" "100" "101" "102" "103" "104" "105" "106" "107" "108"
#> [109] "109" "110" "111" "112" "113" "114" "115" "116" "117" "118" "119" "120"
#> [121] "121" "122" "123" "124" "125"