readBamFileAsGRanges {chromstaR} | R Documentation |
Import aligned reads from a BAM file into a GRanges-class
object.
readBamFileAsGRanges(bamfile, bamindex = bamfile, chromosomes = NULL, pairedEndReads = FALSE, remove.duplicate.reads = FALSE, min.mapq = 10, max.fragment.width = 1000, blacklist = NULL, what = "mapq")
bamfile |
A sorted BAM file. |
bamindex |
BAM index file. Can be specified without the .bai ending. If the index file does not exist it will be created and a warning is issued. |
chromosomes |
If only a subset of the chromosomes should be imported, specify them here. |
pairedEndReads |
Set to |
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 due to mapping errors of paired end reads. |
blacklist |
A |
what |
A character vector of fields that are returned. Uses the |
A GRanges-class
object containing the reads.
## Get an example BAM file with ChIP-seq reads bamfile <- system.file("extdata", "euratrans", "lv-H3K4me3-BN-female-bio1-tech1.bam", package="chromstaRData") ## Read the file into a GRanges object reads <- readBamFileAsGRanges(bamfile, chromosomes='chr12', pairedEndReads=FALSE, min.mapq=10, remove.duplicate.reads=TRUE) print(reads)