easyRNASeq-summarization-internal-methods: Internal count and summarization methods
In easyRNASeq: Count summarization and normalization for RNA-Seq data

Description Usage Arguments Value Author(s) See Also

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

1	.bestExonSummarization(obj)

`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`.

.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.