determineTSR-methods: *determineTSR*

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

Description

determineTSR Identifies TSRs from entire TSS datasets as specified.

Usage

determineTSR(
  experimentName,
  n.cores,
  tssSetType,
  tssSet,
  tagCountThreshold,
  clustDist,
  ...
)

## S4 method for signature 
## 'tssObject,numeric,character,character,numeric,numeric'
determineTSR(
  experimentName,
  n.cores = 1,
  tssSetType = c("replicates", "merged"),
  tssSet = "all",
  tagCountThreshold = 1,
  clustDist = 20,
  writeTable = FALSE,
  mixedorder = FALSE
)

Arguments

experimentName	an object of class tssObject containing information in slot @tssTagData
n.cores	the number of cores to be used for this job. ncores=1 means serial execution of function calls (numeric)
tssSetType	specifies the set to be clustered. Options are "replicates" or "merged". (character)
tssSet	default is "all"; if a single TSS dataset is desired, specify tssSet number (character)
tagCountThreshold	the number of TSSs required at a given position for it to be considered in TSR identification. (numeric)
clustDist	the maximum distance of TSSs between two TSRs in base pairs. (numeric)
writeTable	specifies whether the output should be written to a table. (logical)
mixedorder	a logical specifying whether the sequence names should be ordered alphanumerically in the output table ("10" following "9" rather than "1"). (logical)

Value

creates a list of GenomicRanges-containing TSR positions in slot @tsrData of the returned tssObject object

Note

An example similar to this one can be found in the vignette (/inst/doc/TSRchitect.Rmd)

Examples

load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect"))
tssObjectExample <- determineTSR(experimentName=tssObjectExample, n.cores=1,
tssSetType="replicates", tssSet="1", tagCountThreshold=25, clustDist=20,
writeTable=FALSE)

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