makeGRangesFromTSR-methods: *makeGRangesFromTSR*

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

Description

makeGRangesFromTSR creates a GRanges object from a specified TSR data set

Usage

makeGRangesFromTSR(experimentName, tsrSetType, tsrSet = 1)

## S4 method for signature 'tssObject,character,numeric'
makeGRangesFromTSR(experimentName, tsrSetType, tsrSet = 1)

Arguments

experimentName	an 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 (numeric).

Value

An object of class GRanges containing the specified TSR data set. Headers include 'seqnames', 'ranges' (including start and end), 'strand', 'name' (TSR ID) and 'score' (Shape Index/SI) value

Note

For more information on the GRanges class, please visit: http://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/GenomicRanges/html/GRanges-class.html

Examples

load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect"))
makeGRangesFromTSR(experimentName=tssObjectExample, tsrSetType="replicates",
tsrSet=1)

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