findTailsByPeaks: Find tail positions around/within peak ranges

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

Find tail positions around/within peak ranges

Description

Find the precise positions with polyA tails within d nt of peak ranges, given a peaksfile recording peak ranges. This function narrows the search range of tails to peak ranges to speed up tail searching, which is useful for large BAM file.

Usage

findTailsByPeaks(bamfile, peaksfile, d = 200, tailsfile = NULL, ...)

Arguments

bamfile	A BAM file which needs the index file (.bai).
peaksfile	The path of the peaks.saf file generated by generateSAF.
d	Add a 5' and 3' margin of d nt to each peak to search tails. Default is 200.
tailsfile	if not NULL then output to tailsfile, and return the tailsfile name.
...	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 recording tail positions with chr/strand/coord/count; or tailsfile name (if tailsfile not NULL).

Examples

## Not run: 
findTailsByPeaks(bamfile, peaksfile, d=500)
findTailsByPeaks(bamfile, peaksfile, d=500, tailsfile='output.tails')

## End(Not run)

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