detTSR-methods: detTSR

In TSRchitect: Promoter identification from large-scale TSS profiling data

Description

An internal function, which is invoked using the user-level function determineTSR that identifies TSRs from the selected tssSet (Internal function)

Usage

detTSR(experimentName, tssSetType, tssSet = 1, tagCountThreshold, clustDist)

## S4 method for signature 'tssObject,character,numeric,numeric,numeric'
detTSR(
  experimentName,
  tssSetType,
  tssSet = 1,
  tagCountThreshold = 1,
  clustDist
)

Arguments

experimentName	- a S4 object of class tssObject containing information in slot tssTagData
tssSetType	- specifies the set to be clustered. Options are "replicates" or "merged"
tssSet	- number of the dataset to be analyzed
tagCountThreshold	- number of TSSs required at a given position
clustDist	- maximum distance of TSSs between two TSRs (in base pairs)

Value

via the user-level function determineTSR, creates a list of GenomicRanges objects containing TSR positions in slot 'tsrData' on the tssObject object

TSRchitect documentation built on Nov. 8, 2020, 8:11 p.m.