SVexpression_duo_trio: Extract Read counts for genes that are near or overalapping...

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

Extract Read counts for genes that are near or overalapping SVs.

Description

Extract Read counts for genes that are near or overalapping SVs.

Usage

SVexpression_duo_trio(
  input_fmt_SV = c("Text", "dataFrame"),
  smapdata,
  smappath,
  input_fmt_RNASeq = c("Text", "dataFrame"),
  RNASeqData,
  RNASeqPATH,
  outputfmt = c("Text", "datFrame"),
  pattern_Proband = NA,
  pattern_Mother = NA,
  pattern_Father = NA,
  EnzymeType = c("SVMerge", "SE")
)

Arguments

input_fmt_SV	character. genes that are upstream and/or downstream of SV. input_fmt_RNASeq
smapdata	dataframe. smap data in dataframe format.
smappath	character. smap path.
input_fmt_RNASeq	character. input format of RNASEQ data. Text or dataframe.
RNASeqData	character. Expression of the genes.
RNASeqPATH	character. RNASEQ path.
outputfmt	character. Output format choice dataframe or text.
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.
EnzymeType	character. Enzyme used. option "Dual" or "DLE".

Value

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

Examples

## Not run: 
RNASeqDir = system.file("extdata", package="nanotatoR")
returnMethod="dataFrame"
datRNASeq <- RNAseqcombine(RNASeqDir = RNASeqDir,
returnMethod = returnMethod)
smapName="NA12878_DLE1_VAP_solo5.smap"
smap = system.file("extdata", smapName, package="nanotatoR")
datcomp<-overlapnearestgeneSearch(smap = smap,
   bed=bedFile, inputfmtBed = "BED", outpath,
   n = 3, returnMethod_bedcomp = c("dataFrame"),
   input_fmt_SV = "Text",
   EnzymeType = "SVMerge",
   bperrorindel = 3000,
   bperrorinvtrans = 50000)
datRNASeq1 <- SVexpression(
    input_fmt_SV=c("dataFrame"),
    input_fmt_RNASeq=c("dataFrame"),
    RNASeqData = datRNASeq,
    outputfmt=c("datFrame"),
    pattern_Proband = "*_P_*", EnzymeType = c("SVMerge"))

## End(Not run)

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