nonOverlappingUPGenes: Extracting terms for genes that overlap SVs

In VilainLab/Nanotator: Next generation structural variant annotation and classification

Extracting terms for genes that overlap SVs

Description

Extracting terms for genes that overlap SVs

Usage

nonOverlappingUPGenes(rr, upgene)

Arguments

rr	character. dataframe with primary genes and terms associated.
upgene	character. genes that overlap the SV.

Value

Dataframe with overlapping genes and terms.

Examples

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)
upgene <- as.character(datcomp$Upstream_nonOverlapGenes_dist_kb)
dataPGUP <- nonOverlappingUPGenes (rr, upgene)

VilainLab/Nanotator documentation built on Aug. 2, 2024, 8:45 p.m.