remove_alt_allele_code_from_split_rows: Update code matrix such that alternative alleles are 0s

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

Description

Input the split matrix where rows that once had multiple annotations on single line are now represented on multiple lines. For the sites that once were multiallelic sites and are now represented as biallelic, thus function will change the contents of varmat_code such that the alternative allele(s) are 0. For example, T -> G, C is split into two lines: T -> G and T -> C. In the code matrix, turn the codes correspoding to the allele C in the row T -> G to 0 and the codes corresponding to the allele G in the row T -> C to 0.

Usage

remove_alt_allele_code_from_split_rows(
  varmat_code_split,
  varmat_allele_split,
  ref,
  var,
  rows_with_mult_var_allele_log
)

Arguments

varmat_code_split	- data.frame where the rows are variants (numeric description variants: numbers ranging from -4 to 3), the columns are genomes, and the row.names are annotations, and each line has a single annotation
varmat_allele_split	- 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, and each line has a single annotation
ref	- character vector length nrow(varmat_code_split) = nrow(varmat_allele_split) indicating the reference allele in terms of the positive strand
var	- character vector length nrow(varmat_code_split) = nrow(varmat_allele_split) indicating the variant allele in terms of the positive strand
rows_with_mult_var_allele_log	- logical vector length nrow(varmat_code_split) = nrow(varmat_allele_split) indicating which rows are multiallelic sites

Value

- varmat_code - data.frame where the rows are variants (numeric description variants: numbers ranging from -4 to 3), the columns are genomes, and the row.names are annotations, and each line has a single annotation where the alternative/minor allele in a biallelic-represrentation of a multiallelic site is now 0

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