overlapnearestgeneSearch {nanotatoR} | R Documentation |
Extracts gene information from bed files
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 )
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. |
Data Frame and Text file. Contains the smap with additional Gene Information.
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,]