classifSumm {ProActive}R Documentation

Summarizes pattern-matching results

Description

Summarizes the list of pattern-matching classifications into a table.

Usage

classifSumm(pileup, bestMatchList, windowSize, mode, chunkSize)

Arguments

pileup

A .txt file containing mapped sequencing read coverages averaged over 100 bp windows/bins.

bestMatchList

A list containing pattern-match information associated with all contigs/chunks classified by 'ProActive()' pattern-matching

windowSize

The number of basepairs to average read coverage values over. Options are 100, 200, 500, 1000 ONLY. Default is 1000.

mode

Either "genome" or "metagenome"

chunkSize

If 'mode'="genome" OR if 'mode'="metagenome" and 'chunkContigs'=TRUE, chunk the genome or contigs, respectively, into smaller subsets for pattern-matching.


[Package ProActive version 0.1.0 Index]