View source: R/scAPAtrap_funlib.R
findPeaks | R Documentation |
Perform peak calling on a BAM file with single strand (+ or -) using the output of loadBpCoverages. It is recommended to use findPeaksByStrand instead.
findPeaks(fullCov, strand, L, maxwidth, cutoff = 10, ...)
fullCov |
The output of loadBpCoverages. |
strand |
strand. |
L |
Read length, used to filter peaks wider than L. |
maxwidth |
Maximum peak width, used to filter peaks narrower than maxwidth. Wider peaks will be splitted to smaller ones. |
cutoff |
The base level coverage cutoff to filter valid peaks with enough coverages, default is 10. |
... |
Arguments passed to other methods and/or advanced arguments. Advanced arguments:
|
A data frame with five columns: chr/start/end/strand/value, with each row being a peak. The value column is the average coverage of peak.
## Not run:
forwardPeaks <-findPeaks(fullcovF, '+', 98, 1000)
reversePeaks <-findPeaks(fullcovR, '-', 98, 1000)
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.