fds-methods: Getter/Setter methods for the FraserDataSet The following...

In FRASER: Find RAre Splicing Events in RNA-Seq Data

Description

Getter/Setter methods for the FraserDataSet

The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object.

samples sets or gets the sample IDs; condition ; nonSplicedReads return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds.

Mapping of chromosome names

Usage

samples(object)

samples(object) <- value

condition(object)

condition(object) <- value

bamFile(object)

bamFile(object) <- value

name(object)

name(object) <- value

strandSpecific(object)

strandSpecific(object) <- value

pairedEnd(object)

pairedEnd(object) <- value

workingDir(object)

workingDir(object) <- value

scanBamParam(object)

scanBamParam(object) <- value

nonSplicedReads(object)

nonSplicedReads(object) <- value

## S4 method for signature 'FraserDataSet'
samples(object)

## S4 replacement method for signature 'FraserDataSet'
samples(object) <- value

## S4 method for signature 'FraserDataSet'
condition(object)

## S4 replacement method for signature 'FraserDataSet'
condition(object) <- value

## S4 method for signature 'FraserDataSet'
bamFile(object)

## S4 replacement method for signature 'FraserDataSet'
bamFile(object) <- value

## S4 method for signature 'FraserDataSet'
name(object)

## S4 replacement method for signature 'FraserDataSet'
name(object) <- value

## S4 method for signature 'FraserDataSet'
workingDir(object)

## S4 replacement method for signature 'FraserDataSet'
workingDir(object) <- value

## S4 method for signature 'FraserDataSet'
strandSpecific(object)

## S4 replacement method for signature 'FraserDataSet'
strandSpecific(object) <- value

## S4 method for signature 'FraserDataSet'
pairedEnd(object)

## S4 replacement method for signature 'FraserDataSet'
pairedEnd(object) <- value

## S4 method for signature 'FraserDataSet'
scanBamParam(object)

## S4 replacement method for signature 'FraserDataSet'
scanBamParam(object) <- value

## S4 method for signature 'FraserDataSet'
nonSplicedReads(object)

## S4 replacement method for signature 'FraserDataSet'
nonSplicedReads(object) <- value

FRASER.mcols.get(x, type = NULL, ...)

FRASER.rowRanges.get(x, type = NULL, ...)

mapSeqlevels(fds, style = "UCSC", ...)

Arguments

object	A FraserDataSet object.
value	The new value that should replace the current one.
x	A FraserDataSet object.
type	The psi type (psi3, psi5 or theta)
...	Further parameters. For mapSeqLevels: further parameters passed to GenomeInfoDb::mapSeqlevels().
fds	FraserDataSet
style	The style of the chromosome names.

Value

Getter method return the respective current value.

Author(s)

Christian Mertes [e-mail]

Ines Scheller [e-mail]

Examples

fds <- createTestFraserDataSet()
samples(fds)
samples(fds) <- 1:dim(fds)[2]
condition(fds)
condition(fds) <- 1:dim(fds)[2]
bamFile(fds) # file.paths or objects of class BamFile
bamFile(fds) <- file.path("bamfiles", samples(fds), "rna-seq.bam")
name(fds)
name(fds) <- "My Analysis"
workingDir(fds)
workingDir(fds) <- tempdir()
strandSpecific(fds)
strandSpecific(fds) <- TRUE
strandSpecific(fds) <- "reverse"
strandSpecific(fds)
scanBamParam(fds)
scanBamParam(fds) <- ScanBamParam(mapqFilter=30)
nonSplicedReads(fds)
rowRanges(fds)
rowRanges(fds, type="theta")
mcols(fds, type="psi5")
mcols(fds, type="theta")
seqlevels(fds)
seqlevels(mapSeqlevels(fds, style="UCSC"))
seqlevels(mapSeqlevels(fds, style="Ensembl"))
seqlevels(mapSeqlevels(fds, style="dbSNP"))

FRASER documentation built on Feb. 3, 2021, 2:01 a.m.