compSmapbed {nanotatoR} | R Documentation |
Extracts gene information from bed files
compSmapbed(smap, bed, inputfmtBed = c("BED", "BNBED"), outpath, n = 3, returnMethod_bedcomp = c("Text", "dataFrame"))
smap |
character. Path to SMAP file. |
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 'print $1,$4,$5,$18,$7' gencode.v19.annotation.gtf>HomoSapienGRCH19.bed |
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. |
Data Frame and Text file. Contains the smap with additional Gene Information.
smapName="F1.1_TestSample1_solo_hg19.smap" smap = system.file("extdata", smapName, package="nanotatoR") bedFile <- system.file("extdata", "Homo_sapiens.Hg19_BN_bed.txt", package="nanotatoR") outpath <- system.file("extdata", package="nanotatoR") datcomp<-compSmapbed(smap, bed=bedFile, inputfmtBed = "BNBED", n = 3, returnMethod_bedcomp = c("dataFrame")) datcomp[1,]