getStats: Get alignment and processing stats from BAM files

In mireia-bioinfo/pipelineNGS: Methods for Epigenetic Data Processing

Get alignment and processing stats from BAM files

Description

Given a Logs/ folder generated by the processing functions in this package, returns the statistics for alignment, chrM, duplication rate and number of peaks called.

Usage

getStats(
  path_logs = "Logs/",
  path_peaks = "Peaks/",
  peak_suffix = "narrowPeak"
)

Arguments

path_logs	Path where the log files from samtools mrkdup are stored.
path_peaks	Path where the peaks are saved.
peak_suffix	Type of the peak files, either narrowPeak or broadPeak

Value

Data.frame with some alignment and processing statistics for all the input samples. When files are PE, it returns the total number of mates, not reads.

Examples

## Not run: 
stats <- getStats(raw_bam=c("path/to/file.bam", "path/to/file2.bam"), path_logs="path/logs")

## End(Not run)

mireia-bioinfo/pipelineNGS documentation built on Jan. 2, 2023, 11:18 a.m.