classifSumm: Summarizes pattern-matching results
In ProActive: Detect Elevations and Gaps in Mapped Sequencing Read Coverage
View source: R/bestMatchListFunctions.R
classifSumm 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.
ProActive documentation built on April 4, 2025, 12:58 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
View source: R/bestMatchListFunctions.R
| classifSumm | 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. |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.