overlapnearestgeneSearch: Extracts gene information from bed files

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

Description

Extracts gene information from bed files

Usage

overlapnearestgeneSearch(
  smap,
  bed,
  inputfmtBed = c("bed", "BNBED"),
  EnzymeType = c("SVMerge", "SE"),
  outpath,
  n = 3,
  returnMethod_bedcomp = c("Text", "dataFrame"),
  input_fmt_SV = c("Text", "dataFrame"),
  bperrorindel = 3000,
  bperrorinvtrans = 50000
)

Arguments

smap	character or dataFrame depending on the input_fmt_SV argument. If input_fmt_SV= 'Text", it is path to SMAP file. If input_fmt_SV= 'dataFrame", it is a dataframe.
bed	Text. Normal Bed files or Bionano Bed file.
inputfmtBed	character Whether the bed input is UCSC bed or Bionano bed. Note: extract in bed format to be read by bedsv: awk ' if($3 == "gene" && $13 == "gene_status") print $1,$4,$5,$16,$7 else if ($3 == "gene" && $13 == "gene_name") print $1,$4,$5,$14,$7 ' gencode.v33.annotation.gtf >HomoSapienGRCH19.bed
EnzymeType	Character. Type of enzyme. Options SVMerge and SE.
outpath	character Path for the output files.
n	numeric Number of genes to report which are nearest to the breakpoint. Default is 3.
returnMethod_bedcomp	Character. Type of output Dataframe or in Text format.
input_fmt_SV	Character. Type of output Dataframe or in Text format.
bperrorindel	Numeric. base pair error indel.
bperrorinvtrans	Numeric. base pair error invtranslocation.

Value

Data Frame and Text file. Contains the smap with additional Gene Information.

Examples

smapName="GM24385_Ason_DLE1_VAP_trio5.smap"
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)
datcomp[1,]

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