getTSS: Precisely identify TSSs from bam files, paired end bam files,...

In Linlab-slu/TSSr: TSS sequencing data analysis

Precisely identify TSSs from bam files, paired end bam files, bed files, BigWig files, tss files, or tss tables.

Description

getTSS function is used to precisely identify TSSs from multiple input file formats. The files include users' home-made alignment files (bam format) or downloaded files from public databases. See inputFilesType for details on the supported input file formats.

Usage

getTSS(object, sequencingQualityThreshold = 10, 
mappingQualityThreshold = 20, softclippingAllowed = FALSE)

## S4 method for signature 'TSSr'
getTSS(
  object,
  sequencingQualityThreshold = 10,
  mappingQualityThreshold = 20,
  softclippingAllowed = FALSE
)

Arguments

object	A TSSr object.
sequencingQualityThreshold	Used only if inputFilesType == "bam" or "bamPairedEnd", otherwise ignored.
mappingQualityThreshold	Used only if inputFilesType == "bam" or "bamPairedEnd", otherwise ignored.
softclippingAllowed	Used only if inputFilesType == "bam" or "bamPairedEnd". Default is FALSE.

Value

Large List of elements - one element for each sample

Examples

data(exampleTSSr)
#getTSS(exampleTSSr)

Linlab-slu/TSSr documentation built on Oct. 24, 2023, 8:32 p.m.