readCustomBedFile {chromstaR} | R Documentation |
This is a simple convenience function to read a bed(.gz)-file into a GRanges-class
object. The bed-file is expected to have the following fields: chromosome, start, end, name, score, strand
.
readCustomBedFile(bedfile, col.names = c("chromosome", "start", "end", "name", "score", "strand"), col.classes = NULL, skip = 0, chromosome.format = "NCBI", sep = "")
bedfile |
Filename of the bed or bed.gz file. |
col.names |
A character vector giving the names of the columns in the |
col.classes |
A character vector giving the classes of the columns in |
skip |
Number of lines to skip at the beginning. |
chromosome.format |
Desired format of the chromosomes. Either 'NCBI' for (1,2,3 ...) or 'UCSC' for (chr1,chr2,chr3 ...) or |
sep |
Field separator from |
A GRanges-class
object with the contents of the bed-file.
Aaron Taudt
## Get an example BED file bedfile <- system.file("extdata", "liver-H3K4me3-BN-male-bio2-tech1.bed.gz", package="chromstaRData") ## Import the file and skip the first 10 lines data <- readCustomBedFile(bedfile, skip=10)