easyRNASeq internal methods {easyRNASeq} | R Documentation

## Internal methods of RNAseq objects

### 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

[Package easyRNASeq version 2.28.0 Index]