easyRNASeq-RnaSeqParam-class: Class "RnaSeqParam"

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

Description

A class holding all the necessary parameters to process a bam file issued from an RNA-Seq experiment together with the related annotation to compute a count-table using the simpleRNASeq function. The precision slot is used to determine the count unit:

• readsdefault. The standard summarizeOverlaps-methods function is used to extract the read counts

• bpThe easyRNASeq summarization functions are used to extract the read covered bp counts

Objects from the Class

Objects can be created by calls of the form new("RnaSeqParam", ...) or using the RnaSeqParam constructor.

Author(s)

Nicolas Delhomme

See Also

• RnaSeqParam constructor

• RnaSeqParam accessors

• simpleRNASeq function

• AnnotParam

• AnnotParam constructor

• BamParam

• BamParam constructor

• summarizeOverlaps-methods

• easyRNASeq summarization functions

Examples

showClass("RnaSeqParam")

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