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

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'
# }