Removes specific genomic regions (centromeres and telomeres) of all chromosomes

First, drops the 'Feature' and the 'Ratio' columns. Spurious regions are unstable regions that are difficult to map, so we remove them. The hg19_segments.R file contains positions of these regions. We find them in the bam_ratios_frame and, if found, they are removed.

Usage

RemoveSpuriousRegions(bam_ratios_frame, include_chr_X)

Arguments

bam_ratios_frame

A data frame: a cleaned up version of the original bam_ratios.txt file.

include_chr_X

A boolean: whether we search for chromosome X or not.