findPeaks: Perform peak calling on a BAM file

In BMILAB/scAPAtrap: Identification and Quantification of Alternative Polyadenylation Sites from Single-cell RNA-seq Data

Perform peak calling on a BAM file

Description

Perform peak calling on a BAM file with single strand (+ or -) using the output of loadBpCoverages. It is recommended to use findPeaksByStrand instead.

Usage

findPeaks(fullCov, strand, L, maxwidth, cutoff = 10, ...)

Arguments

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: verbose If 'TRUE' basic status updates will be printed along the way. logf If not NULL, then it should be a character string denoting a file name. Then message will be written to 'logf'.

Value

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.

Examples

## Not run: 
forwardPeaks <-findPeaks(fullcovF, '+', 98, 1000)
reversePeaks <-findPeaks(fullcovR, '-', 98, 1000)

## End(Not run)

BMILAB/scAPAtrap documentation built on Oct. 13, 2023, 2:36 a.m.