easyRNASeq (version 2.8.2)

easyRNASeq internal methods: Internal methods of RNAseq objects

Description

These are generic internal methods:

• .catn Just some pretty printing.
• .checkArguments check that the provided argument match one of the formal definition of the function. Stop if not.
• .convertToUCSC convert chromosome names to UCSC compliant ones.
• .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. \item.getName Get the genomicAnnotation object names. Necessary to deal with the different possible annotation object: RangedData, GRanges or GRangesList. \item.getWidth Get the genomicAnnotation withs. Necessary to deal with the different possible annotation object: RangedData, GRanges or GRangesList. \item.list.files check the arguments passed through the ...to select only the valid ones (deprecated). \item.normalizationDispatcher a function to dispatch the normalization depending on the 'outputFormat' chosen by the user. \itemreduce Allow proper dispatch between the intervals and the GenomicRanges reduce function \itemstrand Allow proper dispatch between the genomeIntervals and the GenomicRanges strand function \itemstrand<- Allow proper dispatch between the genomeIntervals and the GenomicRanges strand replace function

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. For .list.files (deprecated), the additional parameters to be filtered for the list.files function.

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