easyRNASeq-RnaSeqParam: RnaSeqParam constructor

In easyRNASeq: Count summarization and normalization for RNA-Seq data

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)

easyRNASeq documentation built on April 30, 2020, 2 a.m.