addTagCountsToTSR-methods: *addTagCountsToTSR*

Description Usage Arguments Value Note Examples

Description

addTagCountsToTSR adds a matrix of tag counts to a set of identified TSRs

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
addTagCountsToTSR(
  experimentName,
  tsrSetType,
  tsrSet = 1,
  tagCountThreshold = 1,
  writeTable = TRUE
)

## S4 method for signature 'tssObject,character,numeric,numeric,logical'
addTagCountsToTSR(
  experimentName,
  tsrSetType,
  tsrSet = 1,
  tagCountThreshold = 1,
  writeTable = TRUE
)

Arguments

experimentName

a S4 object of class tssObject containing information in slot @tssTagData

tsrSetType

specifies the set to be written to file. Options are "replicates" or "merged". (character)

tsrSet

number of the dataset to be processed, where 1 corresponds to the first slot, and so on. (numeric)

tagCountThreshold

number of tags required at a given TSS position in order to be included in the overall count for a TSR (numeric)

writeTable

specifies whether the output should be written to a table. (logical)

Value

a matrix of tag counts and median-normalized tag counts is appended to the data frame of the selected set of identified TSRs in the returned tssObject; note that the number of new columns is twice the number of replicates in the sample

Note

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

Examples

1
2
3
load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect"))
tssObjectExample <- addTagCountsToTSR(experimentName=tssObjectExample,
tsrSetType="merged", tsrSet=1, tagCountThreshold=25, writeTable=FALSE)

BrendelGroup/TSRchitect documentation built on March 3, 2021, 1:45 a.m.