tsrCluster: tsrCluster

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

Description

an internal function that partitions, then clusters TSS data by sequence to create a data frame containing the coordinates of identified TSRs and other associated metrics, including the site and tag counts (nTSSs, nTAGs), TSR width and (modified) Shape Index (SI, mSI). tsrCluster is an internal function that is invoked via detTSR(), which in turn is called by the user-level function determineTSR().

Usage

tsrCluster(x, minNbrTAGs = 3, minDist = 20)

Arguments

x	a data frame containing a single slot from either tssCountData or tssCountDataMerged, depending on its invocation by parent function determineTSR()
minNbrTAGs	the minimum number of tags at a given TSS position for a TSS to be included in clustering. (numeric)
minDist	the maximum distance of TSSs between two TSRs in base pairs. (numeric)

Value

A data frame of TSRs with variables

1. seq = sequence identifier (seq)

2. start = start of TSR (num)

3. end = end of TSR (num)

4. strand = + or - (factor)

5. nTSSs = count of TSSs (num)

6. nTAGs = count of tags (num)

7. tsrPeak = maximum tag count fraction for all TSS positions in the TSR (num)

8. tsrWdth = width of TSR (num)

9. tsrTrq = TSR torque; measure of TSR balance (num)

10. tsrSI = shape index value of TSR (num)

11. tsrMSI = modified shape index value of TSR (num)

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