label CN segments based on relative chromosomal positions

Uses centromere and telomere coordinates to label where a segment sits on a chromosome, relative to telomeres and centromeres.

Usage

mark_segs_chromosome_span(
  segs_df,
  min_bound_distance = 5e+05,
  min_span_of_chrom = 0.9,
  min_span_of_arm = 0.9,
  version = c("hg19", "hg38"),
  acro_fix_whole_chrom = FALSE
)

Arguments

segs_df

dataframe of CN segments

min_bound_distance

integer. Distance to adjacent feature to be considered associated with that feature.

min_span_of_chrom

float. Proportion of the chromosome to cover to be considered a whole chromosome segment.

min_span_of_arm

float. Proportion of arm to cover to be considered an arm segment.

version

string. hg19 (default) or hg38

acro_fix_whole_chrom.

boolean. Whether to reset acrocentric chromosome CN segments to "whole-chrom" if they span futher than the Q arm. Honestly, probably not useful

Value

input dataframe, annotated with segment scale information. Primary column of interest being seg_span_event.

Details

Possible categories are:

1. telomere bound (telo-bound) - segment touches a telomere

2. centromere bound (centro-bound) - segment touches or crosses the centromere

3. arm (arm) - segment spans a whole are (*with conditions)

4. whole chromosome (whole-chrom) - segment spans the entire chromosome (*with conditions)

5. intersitial (inter) - occuring within the chromosome, not touching the centromere, telomeres, and not big enough to be an entire arm.

You can set a min_bound_distance which reflects how close a feature needs to be to be considered "touching". For example, we can considere a segment telomere bound if within traditional 1 DLP bin by setting this distance to 500k (default). This allows for some level of measurement error.

Users can also set the proportion of the arm or whole chromosome a segment needs to span to be considered either category. Default is spaning 90% of either feature. Meaning, if the segment (end - start)/arm_length is at least 90% of the arm_length, the segment is considered an "arm" spanning segment.

This function runs several other functions including: add_chromosome_length(), add_centromere_locations(), and add_telomere_positions().