nonOverlapRNAseq: Extract Read counts for genes that are near SVs.

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

Extract Read counts for genes that are near SVs.

Description

Extract Read counts for genes that are near SVs.

Usage

nonOverlapRNAseq(
  gnsNonOverlap,
  SVID,
  RNASeqData,
  pattern_Proband = NA,
  pattern_Mother = NA,
  pattern_Father = NA
)

Arguments

gnsNonOverlap	character. genes that are upstream and/or downstream of 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)
gnsNonOverlap <- c("DDX11L1", "MIR1302-2HG", "OR4G4P")
SVID = 397
datgnnonovrlap <- nonOverlapRNAseq(gnsNonOverlap = gnsNonOverlap,
SVID = SVID, RNASeqData = datRNASeq,
pattern_Proband = "*_P_*")

VilainLab/nanotatoR documentation built on Aug. 3, 2024, 12:46 a.m.