easyRNASeq-BamParam: BamParam constructor

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

Description

This constructs a BamParam object. The default parameters are derived from the currently most common RNA-Seq experimental use-case and are detailed below:

• paired is TRUE, i.e. paired-end sequencing is expected.

• stranded is FALSE i.e. stranded sequencing is not expected.

• yieldSize is set to 1,000,000. This is the amount of reads iteratively processed from the bam file stream. It is a compromise between speed, process-parallelization and memory usage.

Usage

## S4 method for signature 'ANY'
BamParam(
  paired = TRUE,
  stranded = FALSE,
  strandProtocol = c("reverse", "forward"),
  yieldSize = 1000000L
)

Arguments

paired	boolean whether the BAM file contains paired-end data or not
stranded	boolean whether the reads are strand specific
strandProtocol	factor with values 'reverse' and 'forward' specifying the type of strand specificity protocol. 'reverse', the reads are on the opposite strand to the gene; typical for Illumina TRUSEQ strand-specific protocol.
yieldSize	the amount of reads to be streamed at a time. Default to 1M

Details

Calling the constructor without argument result in the default parameter described above to be returned. Calling the constructor with any parameter will affect the value of the selected parameters, leaving the other parameters unaffected.

Examples

# the defaults
BamParam()

# change the default
BamParam(paired=FALSE)
BamParam(stranded=TRUE,yieldSize=1L)
BamParam(stranded=TRUE,strandProtocol="forward",yieldSize=1L)

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