club_signature_counts: Club signatures accounting for the strand break and strand...

In kkdey/aRchaic.site: Visualization, Exploration and Clustering of Ancient vs Modern BAM mutation patterns

Description

Function for clubbing signatures from the two strands to remove strnad bias. An example is G->A and C->T are clubbed into C->T to remove the bias due to whether 5' or 3' ends of the strands has been sequenced.

Usage

club_signature_counts(signature_counts, flanking_bases = 1)

Arguments

signature_counts	The matrix of counts of all signatures as produced by aggregate_bin_counts.
flanking_bases	The number of flanking bases. Defaults to 2.

Value

Returns a matrix of clubbed signatures. The default choice of the mutation signatures are C->T, C->A, C->G, T->A, T->C and T->G. The other sets of mutations like G->A are clubbed to C->T to remove strand bias.

kkdey/aRchaic.site documentation built on May 20, 2019, 10:31 a.m.