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

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

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 Oct. 9, 2021, 8:59 p.m.