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

`getTSS.Rd`

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.

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

    # S4 method for TSSr
    getTSS(object, sequencingQualityThreshold = 10, mappingQualityThreshold = 20)

## 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.

## Examples

    # \donttest{
    getTSS(exampleTSSr)#>
    #> Reading in file: S01.sorted.bam...#> Error in value[[3L]](cond): failed to open BamFile: file(s) do not exist:
    #>   'S01.sorted.bam'# }