OverlapRNAseq: Extract Read counts for genes that overlap SVs.

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

Extract Read counts for genes that overlap SVs.

Description

Extract Read counts for genes that overlap SVs.

Usage

OverlapRNAseq(
  gnsOverlap,
  SVID,
  RNASeqData,
  pattern_Proband = NA,
  pattern_Mother = NA,
  pattern_Father = NA
)

Arguments

gnsOverlap	character. genes that overlap SV.
SVID	character. ID of the SVs.
RNASeqData	character. Expression of the genes.
pattern_Proband	character. Pattern to identify the proband reads.
pattern_Mother	character. Pattern to identify the mother reads.
pattern_Father	character. Pattern to identify the father reads.

Value

Text or Dataframe containing TPM read counts of genes in the family.

Examples

RNASeqDir = system.file("extdata", package="nanotatoR")
returnMethod="dataFrame"
datRNASeq <- RNAseqcombine(RNASeqDir = RNASeqDir,
returnMethod = returnMethod)
gnsOverlap <- c("AGL")
SVID = 397
datgnovrlap <- OverlapRNAseq(gnsOverlap = gnsOverlap,
SVID = SVID, RNASeqData = datRNASeq,
pattern_Proband = "*_P_*")

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