getReference: Save CARMA input parameters

In arnevpladsen/CARMA: Calculate CARMA scores

Description

This function will not be called directly by the user. The function is used by the CARMA function and returns a table with genomic positions for the genomic region in which CARMA scores are calculated.

Usage

getReference(region.type, hg, bin.width, overlap, exclude.x.chrom)

Arguments

region.type	the type of region chosen in which CARMA scores are calculated: "arm", "crom" or "bin".
hg	a data frame containing start and end positions of chromosome arms: hg19 or hg38.
bin.width	the width of the bin region.
overlap	if overlap=TRUE, segments within a chromosome arm will overlap to fit within the chromosome arm. If overlap=FALSE, each bin will widen out or be trimmed a little bit relative the defined bin width to fit the chromosome arm.
exclude.x.chrom	if exclude.x.chrom=TRUE, the X chromosome is excluded in the output file.

Value

A data frame defining the start and end position for the genomic regions in which CARMA scores are calculated.

arnevpladsen/CARMA documentation built on Dec. 19, 2021, 4:39 a.m.