Remove or set a mask for relative CN bins (QDNAseq object)
FilterCNs.RdRemove or set a mask for relative CN bins
Usage
FilterCNs(
cnobj,
filter_by = NULL,
genome = "hg19",
minimum_overlap = 5000,
removebins = FALSE,
maskgaps = FALSE,
maskcomCNVs = FALSE,
maskname = "mask1"
)Arguments
- cnobj
QDNASeq object containing the relative copy number calls as well as the segmented relative copy number calls
- filter_by
Optional Dataframe containing genomic regions to filter/mask. One region expected per row.
Expected columns:
chr start end etc. etc.- genome
A character string of the reference genome used. ex "hg38"
- minimum_overlap
An integer designating the number minimum number of overlapping bases for a bin to be removed.
- removebins
A Logical. If TRUE then remove bins overlapping the indicated regions.
- maskgaps
A Logical. If TRUE then remove bins overlapping the centromeric and telomeric regions. Be sure to indicate the correct reference genome.
- maskcomCNVs
A Logical. If TRUE then remove bins overlapping commonly copy-number variant regions in this organism. Be sure to indicate the correct reference genome.
- maskname
A character string for the name to be used in case of setting a mask. Set this field if providing a DF to the filter_by parameter.