chrome_map: Calculate shared and not shared lengths.

In rmunoz12/chromeR: Visualizing IBD Segments on Chromosomes

Description

chrome_map returns a dataframe with shared and not shared regions.

Usage

chrome_map(data, key, chromosome, bp_start, bp_end, threshold = 2e+05)

Arguments

data	Dataframe with key, chromosome, bp_start, and bp_end columns. Each row describes an IBD segment.
key	String identifying the column in data that uniquely identifies the pair of individuals corresponding to each IBD segment.
chromosome	String indentifying the column in data that indicates the chromosome of each IBD segment.
bp_start	String indentifying the column in data that indicates the starting basepair of each IBD segment.
bp_end	String indentifying the column in data that indicates the ending basepair of each IBD segment.
threshold	Numeric value, greater than or equal to 0 for which a gap should be classified as a "merge."

Details

Based on a set of IBD segments, chrome_map calculate the lengths (in basepairs) of the share segments as well as any unshared areas in each chromosome (i.e., gaps). In addition, the threshold parameter can be used to identifiy areas that are small (which chrome_map will then classify as "merge").

Examples

data(test_ibd_segments)
chrome_map(test_ibd_segments, "result_id", "chromosome", "bp_start", "bp_end")

rmunoz12/chromeR documentation built on May 27, 2019, 9:56 a.m.