bed2positions: Unwrap a list of genomic intervals into a list of loci...
In abemus: Adaptive Base Error Model in Ultra-Deep Sequencing Data

Description Usage Arguments Value Examples

Unwrap a list of genomic intervals into a list of loci grouped by chromosome.

1	bed2positions(targetbed, chrom_to_extract, get_only_chromosomes = FALSE)

`targetbed`	Genomic regions in the BED tab-delimited format.
`chrom_to_extract`	The chromosome name to extract as i.e. "chr1" or "1" accordingly with BED file annotation
`get_only_chromosomes`	Set TRUE to return only the list of `chromosomes` present in the `targetbed`. default: FALSE

PosByChrom: A list of data.frames (each row is a locus) one for each chromosome present in the targetbed.

chromosomes: A vector listing chromosomes present in the targetbed.

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targetbed <- system.file("extdata", "regions_toy.bed",package = "abemus")
chromosomes <- bed2positions(targetbed = targetbed,chrom_to_extract="8")
targetbp_list <- bed2positions(targetbed = targetbed,get_only_chromosomes = TRUE)