readBedFileAsGRanges {chromstaR} | R Documentation |
Import aligned reads from a BED file into a GRanges-class
object.
readBedFileAsGRanges(bedfile, assembly, chromosomes = NULL, remove.duplicate.reads = FALSE, min.mapq = 10, max.fragment.width = 1000, blacklist = NULL)
bedfile |
A file with aligned reads in BED-6 format. The columns have to be c('chromosome','start','end','description','mapq','strand'). |
assembly |
Please see |
chromosomes |
If only a subset of the chromosomes should be imported, specify them here. |
remove.duplicate.reads |
A logical indicating whether or not duplicate reads should be removed. |
min.mapq |
Minimum mapping quality when importing from BAM files. Set |
max.fragment.width |
Maximum allowed fragment length. This is to filter out erroneously wrong fragments. |
blacklist |
A |
A GRanges-class
object containing the reads.
## Get an example BED file with single-cell-sequencing reads bedfile <- system.file("extdata", "liver-H3K4me3-BN-male-bio2-tech1.bed.gz", package="chromstaRData") ## Read the file into a GRanges object data(rn4_chrominfo) reads <- readBedFileAsGRanges(bedfile, assembly=rn4_chrominfo, chromosomes='chr12', min.mapq=10, remove.duplicate.reads=TRUE) print(reads)