aggregate_signature_counts: Aggregate mutationFileFormat for multiple files into a matrix...

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

Description

For each file of the directory, performs the damage.build.counts function and aggregates the data into counts matrix format with the number of rows equal to the number of files in the directory and the columns corresponding to the number of different mutation signatures recorded. The files must be in .csv format.

Usage

aggregate_signature_counts(dir, breaks = NULL, flanking_bases = 1,
  output_rda = NULL)

Arguments

dir	The directory containing the files that are to be read and aggregated over.
breaks	The breaks used for the damage.build.counts function.
flanking_bases	The number of flanking bases. Defaults to 2.
output_rda	If non-NULL, the output matrix is stored in the path provided (should end with .rda).

Value

Returns a matrix of aggregate counts of each signature for each file arranged along a row of the matrix. The number of rows correspond to the number of files in the directory and the number of columns equalling the number of distinct mutation signatures.

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