briefly in a current project i tried to implement the R package motifbreakR, in order to identify putative SNPs from somatic variant calling, that could cause an "important" disruption in TF-binding sites. The first part of my code chunk, is for reading the SNPs included in the relative vcf file i tried as an initial example:
library(motifbreakR)
library(BSgenome)
vcf_files <- list.files(pattern = ".vcf", full.names = TRUE)
list.files()
[1] "LY14_01.recode.snpEff_annotated.filtered.snps.recode.dbnsfp_anno (1).vcf"
snps.vcf <- snps.from.file(file=vcf_files,search.genome =BSgenome.Hsapiens.UCSC.hg38,format = "vcf")
Error in info(snps) : could not find function "info"
In addition: Warning message:
In .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Greek_Greece.1253 LC_CTYPE=Greek_Greece.1253
[3] LC_MONETARY=Greek_Greece.1253 LC_NUMERIC=C
[5] LC_TIME=Greek_Greece.1253
attached base packages:
[1] stats4 parallel grid stats graphics grDevices utils datasets
[9] methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg38_1.4.1 BSgenome_1.48.0
[3] rtracklayer_1.40.3 GenomicRanges_1.32.3
[5] GenomeInfoDb_1.16.0 motifbreakR_1.10.0
[7] MotifDb_1.22.0 Biostrings_2.48.0
[9] XVector_0.20.0 IRanges_2.14.10
[11] S4Vectors_0.18.3 BiocGenerics_0.26.0
[13] BiocInstaller_1.30.0
Thus, perhaps there is a bug with the function readVcf ? i have also created a relative post in the Bioconductor Support Group:
Dear @Simon-Coetzee & @dennishazelett ,
briefly in a current project i tried to implement the R package motifbreakR, in order to identify putative SNPs from somatic variant calling, that could cause an "important" disruption in TF-binding sites. The first part of my code chunk, is for reading the SNPs included in the relative vcf file i tried as an initial example:
Thus, perhaps there is a bug with the function readVcf ? i have also created a relative post in the Bioconductor Support Group:
https://support.bioconductor.org/p/110110/#110802
Thank you in advance,
Efstathios-Iason Vlachavas