Hi Everyone!
I have a problem with using rDGIdb looking for possible drug candidates. I want to use the option of VCF input and I am following the code described in https://bioconductor.org/packages/release/bioc/vignettes/rDGIdb/inst/doc/vignette.pdf. However it always gives me an error in the end:
library(VariantAnnotation)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
vcf <- readVcf("somatic-wgs.vcf.gz", "hg19")
seqlevels(vcf) <- paste("chr", seqlevels(vcf), sep = "")
rd <- rowRanges(vcf)
loc <- locateVariants(rd, txdb, CodingVariants())
And the error is: Error in compatibleSeqnames(rep(seqnames(x), elementNROWS(y)), seqnames(y@unlistData)) : Level set of 'x' must be subset of that of 'y', or vice versa
I checked the seqlevels of my vcf file and TxDB as well:
seqlevels(vcf))
[1] "chr1" "chr2" "chr3" "chr4" "chr5"
[6] "chr6" "chr7" "chr8" "chr9" "chr10"
[11] "chr11" "chr12" "chr13" "chr14" "chr15"
[16] "chr16" "chr17" "chr18" "chr19" "chr20"
[21] "chr21" "chr22" "chrX" "chrY" "chrMT"
[26] "chrGL000207.1" "chrGL000226.1" "chrGL000229.1" "chrGL000231.1" "chrGL000210.1"
[31] "chrGL000239.1" "chrGL000235.1" "chrGL000201.1" "chrGL000247.1" "chrGL000245.1"
[36] "chrGL000197.1" "chrGL000203.1" "chrGL000246.1" "chrGL000249.1" "chrGL000196.1"
[41] "chrGL000248.1" "chrGL000244.1" "chrGL000238.1" "chrGL000202.1" "chrGL000234.1"
[46] "chrGL000232.1" "chrGL000206.1" "chrGL000240.1" "chrGL000236.1" "chrGL000241.1"
[51] "chrGL000243.1" "chrGL000242.1" "chrGL000230.1" "chrGL000237.1" "chrGL000233.1"
[56] "chrGL000204.1" "chrGL000198.1" "chrGL000208.1" "chrGL000191.1" "chrGL000227.1"
[61] "chrGL000228.1" "chrGL000214.1" "chrGL000221.1" "chrGL000209.1" "chrGL000218.1"
[66] "chrGL000220.1" "chrGL000213.1" "chrGL000211.1" "chrGL000199.1" "chrGL000217.1"
[71] "chrGL000216.1" "chrGL000215.1" "chrGL000205.1" "chrGL000219.1" "chrGL000224.1"
[76] "chrGL000223.1" "chrGL000195.1" "chrGL000212.1" "chrGL000222.1" "chrGL000200.1"
[81] "chrGL000193.1" "chrGL000194.1" "chrGL000225.1" "chrGL000192.1"
(seqlevels(txdb))
[1] "chr1" "chr2" "chr3"
[4] "chr4" "chr5" "chr6"
[7] "chr7" "chr8" "chr9"
[10] "chr10" "chr11" "chr12"
[13] "chr13" "chr14" "chr15"
[16] "chr16" "chr17" "chr18"
[19] "chr19" "chr20" "chr21"
[22] "chr22" "chrX" "chrY"
[25] "chrM" "chr1_gl000191_random" "chr1_gl000192_random"
[28] "chr4_ctg9_hap1" "chr4_gl000193_random" "chr4_gl000194_random"
[31] "chr6_apd_hap1" "chr6_cox_hap2" "chr6_dbb_hap3"
[34] "chr6_mann_hap4" "chr6_mcf_hap5" "chr6_qbl_hap6"
[37] "chr6_ssto_hap7" "chr7_gl000195_random" "chr8_gl000196_random"
[40] "chr8_gl000197_random" "chr9_gl000198_random" "chr9_gl000199_random"
[43] "chr9_gl000200_random" "chr9_gl000201_random" "chr11_gl000202_random"
[46] "chr17_ctg5_hap1" "chr17_gl000203_random" "chr17_gl000204_random"
[49] "chr17_gl000205_random" "chr17_gl000206_random" "chr18_gl000207_random"
[52] "chr19_gl000208_random" "chr19_gl000209_random" "chr21_gl000210_random"
[55] "chrUn_gl000211" "chrUn_gl000212" "chrUn_gl000213"
[58] "chrUn_gl000214" "chrUn_gl000215" "chrUn_gl000216"
[61] "chrUn_gl000217" "chrUn_gl000218" "chrUn_gl000219"
[64] "chrUn_gl000220" "chrUn_gl000221" "chrUn_gl000222"
[67] "chrUn_gl000223" "chrUn_gl000224" "chrUn_gl000225"
[70] "chrUn_gl000226" "chrUn_gl000227" "chrUn_gl000228"
[73] "chrUn_gl000229" "chrUn_gl000230" "chrUn_gl000231"
[76] "chrUn_gl000232" "chrUn_gl000233" "chrUn_gl000234"
[79] "chrUn_gl000235" "chrUn_gl000236" "chrUn_gl000237"
[82] "chrUn_gl000238" "chrUn_gl000239" "chrUn_gl000240"
[85] "chrUn_gl000241" "chrUn_gl000242" "chrUn_gl000243"
[88] "chrUn_gl000244" "chrUn_gl000245" "chrUn_gl000246"
[91] "chrUn_gl000247" "chrUn_gl000248" "chrUn_gl000249"
Any suggestions? Thank you!
