easyRNASeq-internal-methods: Internal methods of RNAseq objects

In easyRNASeq: Count summarization and normalization for RNA-Seq data

Description

These are generic internal methods:

• Actual

  • .catn Just some pretty printing.

  • .checkArguments check that the provided argument match one of the formal definition of the function. Stop if not.

  • .extractIRangesList extract an IRanges object from an AlignedRead or a GAlignments object or a list returned by reading a bam file with Rsamtools. It returns a list containing the IRangesList and library size.

  • .getArguments For a given function returns the arguments passed as part of the ... that match that function formals.

  • .getName Get the genomicAnnotation object names. Necessary to deal with the different possible annotation object: GRanges or GRangesList.

  • .getWidth Get the genomicAnnotation withs. Necessary to deal with the different possible annotation object: GRanges or GRangesList.

  • .normalizationDispatcher a function to dispatch the normalization depending on the 'outputFormat' chosen by the user.

  • reduce Allow proper dispatch between the intervals and the GenomicRanges reduce function

  • strand Allow proper dispatch between the genomeIntervals and the GenomicRanges strand function

  • strand<- Allow proper dispatch between the genomeIntervals and the GenomicRanges strand replace function

• Defunct

  • .convertToUCSC convert chromosome names to UCSC compliant ones.

  • .list.files check the arguments passed through the ... to select only the valid ones (defunct).

Usage

.extractIRangesList(obj, chr.sel = c())

Arguments

obj	An RNAseq object, or for the 'normalizationDispatcher', depending on the type: a CountDataSet, a DGEList, a matrix, or an RNAseq object respectively
chr.sel	A list of chromosome to restrict the IRanges spaces returned.
arg	The argument name to check for.
chr.names	The chromosome names, as a character vector, to be converted to UCSC ones
fun	The name of the function
organism	The organism name
type	character string specifying the type of object (normalizationDispatcher)
value	the appropriate strand object (strand and strand<-) or the provided argument value (checkArguments)
x	an object of the GenomicRanges, intervals or genomeIntervals package
...	For .getArguments a list of named parameters to be matched against a function formal definition. For .catn, the values to be printed.

Value

argString	a character string representing these arguments and their value that matched those defined in the formal definition of the function
convertedChrNames	a converted vector of chromosome names
i.range	an IRange object
names	The annotation names, i.e. a combination of exon, feature, transcript and gene
normalized.counts	Depending on the type, a CountDataSet, a DGEList, a NumericList, or NULL respectively

Author(s)

Nicolas Delhomme

easyRNASeq documentation built on April 30, 2020, 2 a.m.