easyRNASeq summarization internal methods {easyRNASeq} | R Documentation

## Internal count and summarization methods

### Description

These are internal methods related to counting and summarizing reads

- For counting reads:

  - .doCount A dispatcher higher level function to count and summarize reads. Externalized so that it can be parallelized.

  - .doBasicCount A function to calculate the counts for 'exons' or 'features'

- For summarizing per genes: these methods are called by the method `geneCounts`. Having performed the `exonCounts` is a pre-requisite.

  - .bestExonSummarization Identify the exon showing the highest coverage.

  - .geneModelSummarization Sum the coverage values of the synthetic exons constituting a gene model.

- For managing the summarized read count structure:

  - .extendCountList extend or create the result count list of matrices

### Usage

    .bestExonSummarization(obj)

### Arguments

`obj` | An object derived from class `RNAseq`
`chr.map` | A data.frame describing the mapping of original chromosome names towards wished chromosome names. See the details in `easyRNASeq`.
`chr.sel` | A vector of chromosome names to subset the final results.
`cList` | list of lists that contain count results
`count` | The feature used to summarize the reads. One of 'exons','features','genes','islands' or 'transcripts'.
`filename` | The full path of the file to use
`filter` | The filter to be applied when loading the data using the "aln" format
`format` | The format of the reads, one of "aln","bam". If not "bam", all the types supported by the ShortRead package are supported too. As of version 1.3.5, it defaults to bam.
`gapped` | Is the bam file provided containing gapped alignments?
`min.cov` | When computing read islands, the minimal coverage to take into account for calling an island
`min.length` | The minimal size an island should have to be kept
`max.gap` | When computing read islands, the maximal gap size allowed between two islands to merge them
`plot` | Whether or not to plot assessment graphs.
`rnaSeq` | An object derived from class `RNAseq`
`summarization` | A character defining which method to use when summarizing reads by genes. So far, only "geneModels" is available.
`silent` | set to TRUE if you do not want messages to be printed out.
`subType` | character string defining a sub type of counts, i.e. for the gene type one of bestExon or geneModel
`type` | .extendCountList: character string specifying the type of count ("exons", "transcripts", "genes" or islands) .doCount: the type of data when using the "aln" format. See the ShortRead library.
`validity.check` | Shall UCSC chromosome name convention be enforced? This is only supported for a set of organisms, which are Dmelanogaster, Hsapiens, Mmusculus and Rnorvegicus; otherwise the argument 'chr.map' can be used to complement it.
`values` | a named vector containing count results
`...` | additional arguments. See the details in `easyRNASeq`.

### Value

- .doCount: a list containing

  - counts: the summarized counts as a matrix of dimension number of genes x 1

  - size: the library size

- .doBasicCount: a vector containing read counts.

- .bestExonSummarization: a vector containing summarized counts.

- .geneModelSummarization: a vector containing summarized counts.

- .extendCountList: a named list of matrices. The names are according to the counting/summarization already performed.

### Author(s)

Nicolas Delhomme

### See Also

- `ShortRead:readAligned`

- `RNAseq` `easyRNASeq`.

[Package easyRNASeq version 2.28.0 Index]