overlappingGenes {nanotatoR} | R Documentation |
Extracting terms for genes that overlap SVs
overlappingGenes(rr, ogene)
rr |
character. dataframe with primary genes and terms associated. |
ogene |
character. genes that overlap the SV. |
Dataframe with overlapping genes and terms.
terms= c("steroid_Gene","steroid synthesis_Gene") genes <- c("NR1H3", "ABCC4") rr <- data.frame(Genes = genes, Terms = terms) smapName="GM24385_Ason_DLE1_VAP_trio5.smap" smap = system.file("extdata", smapName, package="nanotatoR") bedFile <- system.file("extdata", "HomoSapienGRCH19_lift37.bed", package="nanotatoR") outpath <- system.file("extdata", package="nanotatoR") datcomp<-overlapnearestgeneSearch(smap = smap, bed=bedFile, inputfmtBed = "bed", outpath, n = 3, returnMethod_bedcomp = c("dataFrame"), input_fmt_SV = "Text", EnzymeType = "SE", bperrorindel = 3000, bperrorinvtrans = 50000) ogene <- as.character(datcomp$OverlapGenes_strand_perc) datogenes <- overlappingGenes (rr, ogene)