remove_rows_with_no_variants_or_completely_masked: Remove rows with no variants or that are completely masked

In Snitkin-Lab-Umich/snitkitr: Functions Commonly Used in the Snitkin Lab

Description

Removes rows that have no variants (the same allele in every sample +/- N and dash) or rows that are completely masked (all Ns).

Usage

remove_rows_with_no_variants_or_completely_masked(varmat_code, varmat_allele)

Arguments

varmat_code	- data.frame where the rows are variants (numeric description variants: numbers ranging from -4 to 3), the columns are genomes, and therow.names are annotations
varmat_allele	- data.frame where the rows are variants (character description variants: A,C,T,G,N,-), the columns are genomes, and the row.names are annotations

Value

Returns a list with the following elements (in order): 1. varmat_code (class = data.frame) with non-variant rows removed. All rows have at least one sample with a variant. 2. varmat_allele (class = data.frame) with non-variant rows removed. All rows have at least one sample with a variant. 1 and 2 should be the same dimensions and have the same row names. Also writes a file called YEAR_MONTH_DATE_rows_removed_because_no_variants logging the row names of the removed rows.

Snitkin-Lab-Umich/snitkitr documentation built on April 21, 2021, 10:48 a.m.