Closed MingLi-929 closed 1 year ago
add columns to annotatePeak() to fix #193 The columns can help to get the specific columns from database. From the bug reported from #193, users can not get ENSEMBL even if pass in database
columns
library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(EnsDb.Hsapiens.v86) files <- getSampleFiles() txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene Anno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000), TxDb=TxDb.Hsapiens.UCSC.hg19.knownGene, annoDb="EnsDb.Hsapiens.v86") > Anno@anno GRanges object with 1331 ranges and 13 metadata columns: seqnames ranges strand | V4 V5 <Rle> <IRanges> <Rle> | <character> <numeric> [1] chr1 815093-817883 * | MACS_peak_1 295.76 [2] chr1 1243288-1244338 * | MACS_peak_2 63.19 [3] chr1 2979977-2981228 * | MACS_peak_3 100.16 [4] chr1 3566182-3567876 * | MACS_peak_4 558.89 [5] chr1 3816546-3818111 * | MACS_peak_5 57.57 ... ... ... ... . ... ... [1327] chrX 135244783-135245821 * | MACS_peak_1327 55.54 [1328] chrX 139171964-139173506 * | MACS_peak_1328 270.19 [1329] chrX 139583954-139586126 * | MACS_peak_1329 918.73 [1330] chrX 139592002-139593238 * | MACS_peak_1330 210.88 [1331] chrY 13845134-13845777 * | MACS_peak_1331 58.39 annotation geneChr geneStart geneEnd geneLength <character> <integer> <integer> <integer> <integer> [1] Promoter (2-3kb) 1 803451 812182 8732 [2] Promoter (<=1kb) 1 1243994 1247057 3064 [3] Promoter (<=1kb) 1 2976181 2980350 4170 [4] Promoter (<=1kb) 1 3547331 3566671 19341 [5] Promoter (<=1kb) 1 3816968 3832011 15044 ... ... ... ... ... ... [1327] Intron (uc010nrz.2/2.. 23 135251455 135293518 42064 [1328] Promoter (<=1kb) 23 139173826 139175070 1245 [1329] Promoter (1-2kb) 23 139585152 139587225 2074 [1330] Distal Intergenic 23 139585152 139587225 2074 [1331] Distal Intergenic 24 14517915 14533389 15475 geneStrand geneId transcriptId distanceToTSS SYMBOL GENENAME <integer> <character> <character> <numeric> <character> <character> [1] 2 284593 uc001abt.4 -2911 FAM41C FAM41C [2] 1 126789 uc001aed.3 0 PUSL1 PUSL1 [3] 2 440556 uc001aka.3 0 LINC00982 LINC00982 [4] 2 49856 uc001ako.3 0 WRAP73 WRAP73 [5] 1 100133612 uc001alg.3 0 LINC01134 LINC01134 ... ... ... ... ... ... ... [1327] 1 2273 uc004ezn.2 -5634 FHL1 FHL1 [1328] 1 389895 uc031tkm.1 -320 <NA> <NA> [1329] 2 6658 uc004fbd.1 1099 SOX3 SOX3 [1330] 2 6658 uc004fbd.1 -4777 SOX3 SOX3 [1331] 2 352887 uc022cji.1 687612 <NA> <NA> ------- seqinfo: 24 sequences from hg19 genome
after adding columns, users can get the specific columns from database.
Anno1 <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000), TxDb=TxDb.Hsapiens.UCSC.hg19.knownGene, annoDb="EnsDb.Hsapiens.v86", columns=c("ENTREZID", "GENEID", "SYMBOL", "GENENAME")) > Anno1@anno GRanges object with 1331 ranges and 14 metadata columns: seqnames ranges strand | V4 V5 <Rle> <IRanges> <Rle> | <character> <numeric> [1] chr1 815093-817883 * | MACS_peak_1 295.76 [2] chr1 1243288-1244338 * | MACS_peak_2 63.19 [3] chr1 2979977-2981228 * | MACS_peak_3 100.16 [4] chr1 3566182-3567876 * | MACS_peak_4 558.89 [5] chr1 3816546-3818111 * | MACS_peak_5 57.57 ... ... ... ... . ... ... [1327] chrX 135244783-135245821 * | MACS_peak_1327 55.54 [1328] chrX 139171964-139173506 * | MACS_peak_1328 270.19 [1329] chrX 139583954-139586126 * | MACS_peak_1329 918.73 [1330] chrX 139592002-139593238 * | MACS_peak_1330 210.88 [1331] chrY 13845134-13845777 * | MACS_peak_1331 58.39 annotation geneChr geneStart geneEnd geneLength <character> <integer> <integer> <integer> <integer> [1] Promoter (2-3kb) 1 803451 812182 8732 [2] Promoter (<=1kb) 1 1243994 1247057 3064 [3] Promoter (<=1kb) 1 2976181 2980350 4170 [4] Promoter (<=1kb) 1 3547331 3566671 19341 [5] Promoter (<=1kb) 1 3816968 3832011 15044 ... ... ... ... ... ... [1327] Intron (uc010nrz.2/2.. 23 135251455 135293518 42064 [1328] Promoter (<=1kb) 23 139173826 139175070 1245 [1329] Promoter (1-2kb) 23 139585152 139587225 2074 [1330] Distal Intergenic 23 139585152 139587225 2074 [1331] Distal Intergenic 24 14517915 14533389 15475 geneStrand geneId transcriptId distanceToTSS GENEID <integer> <character> <character> <numeric> <character> [1] 2 284593 uc001abt.4 -2911 ENSG00000230368 [2] 1 126789 uc001aed.3 0 ENSG00000169972 [3] 2 440556 uc001aka.3 0 ENSG00000177133 [4] 2 49856 uc001ako.3 0 ENSG00000116213 [5] 1 100133612 uc001alg.3 0 ENSG00000236423 ... ... ... ... ... ... [1327] 1 2273 uc004ezn.2 -5634 ENSG00000022267 [1328] 1 389895 uc031tkm.1 -320 <NA> [1329] 2 6658 uc004fbd.1 1099 ENSG00000134595 [1330] 2 6658 uc004fbd.1 -4777 ENSG00000134595 [1331] 2 352887 uc022cji.1 687612 <NA> SYMBOL GENENAME <character> <character> [1] FAM41C FAM41C [2] PUSL1 PUSL1 [3] LINC00982 LINC00982 [4] WRAP73 WRAP73 [5] LINC01134 LINC01134 ... ... ... [1327] FHL1 FHL1 [1328] <NA> <NA> [1329] SOX3 SOX3 [1330] SOX3 SOX3 [1331] <NA> <NA> ------- seqinfo: 24 sequences from hg19 genome
here we can see the ENSEMBL id
add
columnsto annotatePeak() to fix #193 Thecolumnscan help to get the specific columns from database. From the bug reported from #193, users can not get ENSEMBL even if pass in databaseafter adding
columns, users can get the specific columns from database.here we can see the ENSEMBL id