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

View source: R/RNASEQ_Analysis_Duo_Trio_SVMerge_SE.r

nonOverlapRNAseqR Documentation

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. 2, 2024, 8:45 p.m.