BamParam

BamParam,ANY-method

easyRNASeq BamParam constructor

paired

stranded

yieldSize

This constructs a <code><links4class>BamParam</links4class></code> object.
The default parameters are derived from the currently most 
common RNA-Seq experimental use-case and are detailed below:
<ul><li>paired is TRUE,i.e.paired-end sequencing is expected.</li><li>stranded is FALSEi.e.stranded sequencing is not expected.</li><li>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.</li></ul>

Calculates the coverage of high-throughput short-reads against
    a genome of reference and summarizes it per feature of interest (e.g. exon,
    gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq'
    or 'edgeR' package.

Nicolas Delhomme

easyRNASeq

Count summarization and normalization for RNA-Seq data

easyRNASeq BamParam constructor function

This constructs a <code><linkS4class>BamParam</linkS4class></code> object.
The default parameters are derived from the currently most 
common RNA-Seq experimental use-case and are detailed below:
<ul><li>paired is TRUE,i.e.paired-end sequencing is expected.</li><li>stranded is FALSEi.e.stranded sequencing is not expected.</li><li>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.</li></ul>

easyRNASeq BamParam constructor: BamParam constructor

Description

Usage

Arguments

Details

Examples