easyRNASeq BamParam constructor {easyRNASeq} | R Documentation

## BamParam constructor

### 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)

[Package easyRNASeq version 2.30.0 Index]