createSummarizedExperiment-methods: *createSummarizedExperiment*

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

Description

createSummarizedExperiment creates and reutrns a SummarizedExperiment object from the tag counts on a selected TSR dataset.

Usage

createSummarizedExperiment(
  experimentName,
  tsrSetType = "merged",
  tsrSet = 1,
  samplePrefix
)

## S4 method for signature 'tssObject,character,numeric,character'
createSummarizedExperiment(
  experimentName,
  tsrSetType = "merged",
  tsrSet = 1,
  samplePrefix
)

Arguments

experimentName	an S4 object of class tssObject containing information in slot @tssTagData
tsrSetType	specifies the TSR set to be converted into a SummarizedExperiment object. Options are "replicates" or "merged". (character)
tsrSet	number of the dataset to be processed (numeric).
samplePrefix	the prefix (or prefixes) that match the sample identifiers in the tsrData column. (character)

Value

a summarizedExperiment object from the specified TSR data set that is to be written to your working directory.

Note

For more information on the SummarizedExperiment class, please visit https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html

Examples

load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect"))
createSummarizedExperiment(tssObjectExample, tsrSetType="merged", tsrSet=1,
samplePrefix=c("sample1","sample2"))

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