easyRNASeq RnaSeqParam constructor {easyRNASeq} | R Documentation

## RnaSeqParam constructor

### Description

This constructs a `RnaSeqParam` object, that combines all the necessary parameters for the analysis of RNA-Seq data. As much as possible, these parameters are determined automa-gi/ti-cally. It describes three sets of parameters:

- parameters describing the annotation

- parameters describing the BAM files, i.e. the type of sequencing that was conducted.

- parameters describing how the counting should be done.

The first two are provided through sepcific objects: `AnnotParam` and `BamParam` respectively. The third one is a set constituted of:

- countBy: the feature per which the counts should be summarized ( exon, transcript or gene. A forth possibility - feature - can be used to define arbitrary genomic loci)

- precision: the precision at which the counts should be performed: bp or reads. bp used to be the default in the `easyRNASeq` package, whereas now reads is, following the Bioconductor main stream development.

The default parameters for the `BamParam` parameter are derived from the currently most common RNA-Seq experimental use-case: strand-specific paired-end Illumina sequencing. See the respective manual pages of `AnnotParam` and `BamParam` for more details.

### Usage

    ## S4 method for signature 'ANY'
    RnaSeqParam(
      annotParam = AnnotParam(),
      bamParam = BamParam(),
      countBy = c("exons", "features", "genes", "transcripts"),
      precision = c("read", "bp")
    )

### Arguments

`annotParam` | An object derived from class `AnnotParam`.
`bamParam` | An object derived from class `BamParam`.
`countBy` | TODO
`precision` | A character value, either 'read' or 'bp' that defines the precision at which counting is done, either per read or per covered bp. 'read' is the default.

### Examples

    annotParam <- AnnotParam(
                    datasource=system.file(
                                    "extdata",
                                    "Dmel-mRNA-exon-r5.52.gff3",
                                    package="RnaSeqTutorial"))

    ## create the RnaSeqParam
    rsp <- RnaSeqParam(annotParam=annotParam)

    ## change some defaults
    RnaSeqParam(countBy="features",annotParam=annotParam)
    RnaSeqParam(bamParam=BamParam(stranded=TRUE,yieldSize=1L),annotParam=annotParam)

[Package easyRNASeq version 2.24.1 Index]