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]