Adds a column for the chromosome arm in which each segment is in.

More specifically, iterates through all the segments, and using genomic data for the middle positions of all chromosomes, it determines whether the segment is to the left or to the right of the middle position. For example, if a segment is in chromosome 5 and is to the left of the middle position, it is in chromosome arm 1. If it were to the right instead, then its chromosome arm would be 1.5.

Note that most of this iterative process is done in the AddChromosomeArmHelper helper.

Usage

AddChromosomeArm(bam_ratios_frame, include_chr_X)

Arguments

bam_ratios_frame

A data frame: the cleaned up version of the bam_ratios.txt file. In the algorithm, this segment data has already had its spurious regions removed.

include_chr_X

A boolean: True if we include chromosome X/23, False otherwise.