classify_variants: Given a pile of variants from freebayes and friends, make a...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Given a pile of variants from freebayes and friends, make a table of what changed.

Description

My post-processor of the results from mpileup/freebayes provides some hopefully fun output files. This function seeks to leverage them into tables which might be fun to look at.

Usage

classify_variants(
  metadata,
  coverage_column = "bedtoolscoveragefile",
  variants_column = "freebayesvariantsbygene",
  min_missing = 100
)

Arguments

metadata	Usually the result of gather_preprocessing_metadata(), but whatever it is, it should have a column containing the observed coverage and observed variants as a table.
coverage_column	Metadata column name containing coverage information from bedtools in a tabular format.
variants_column	Metadata column name containing the variants/gene.
min_missing	Bin size above which to call a region missing from one or more samples when looking for large-scale deletions using coverage information.

Value

List containing some fun stuff.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.