SVexpression_solo: Annotating the Overlapping and Non-Overlapping genes with...

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

Description

Annotating the Overlapping and Non-Overlapping genes with RNAseq expression

Usage

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

Arguments

input_fmt_SV	character. Input format of the SV data.Options "Text" or "DataFrame".
smapdata	dataframe. SV data dataframe.
smappath	character. smap path.
input_fmt_RNASeq	character. Input format of the RNASeq data. Options "Text" or "DataFrame"..
RNASeqData	dataFrame. RNAseq data with gene names.
RNASeqPATH	character. RNAseq dataset path .
outputfmt	character. Output format of the result. Options "Text" or "DataFrame"..
pattern_Proband	character. Pattern for proband.
EnzymeType	character. Enzyme used. option "SVMerge" or "SE".

Value

Dataframe Annotated datafreme with RNASeq data.

Examples

RNASeqDir = system.file("extdata", package="nanotatoR")
returnMethod="dataFrame"
datRNASeq <- RNAseqcombine_solo(RNASeqDir = RNASeqDir,
returnMethod = returnMethod)
smapName="NA12878_DLE1_VAP_solo5.smap"
smap = system.file("extdata", smapName, package="nanotatoR")
smap = system.file("extdata", smapName, package="nanotatoR")
bedFile <- system.file("extdata", "HomoSapienGRCH19_lift37.bed", package="nanotatoR")
outpath <- system.file("extdata", package="nanotatoR")
datcomp<-overlapnearestgeneSearch(smap = smap, 
    bed=bedFile, inputfmtBed = "bed", outpath, 
    n = 3, returnMethod_bedcomp = c("dataFrame"), 
    input_fmt_SV = "Text",
    EnzymeType = "SE", 
    bperrorindel = 3000, 
    bperrorinvtrans = 50000)
datRNASeq1 <- SVexpression_solo (input_fmt_SV=c("dataFrame"),
    smapdata = datcomp,
    input_fmt_RNASeq=c("dataFrame"),
    RNASeqData = datRNASeq,
    outputfmt=c("datFrame"),
    pattern_Proband = "*_P_*", EnzymeType = c("SE"))
datRNASeq1[1,]

VilainLab/Nanotator documentation built on Oct. 9, 2021, 8:59 p.m.