CreateMarvelObject {MARVEL}

Create Marvel object for plate-based RNA-sequencing data

Description

Creates an S3 object named Marvel for downstream analysis, specifically for plate-based RNA-sequencing data.

Usage

CreateMarvelObject(
  SplicePheno = NULL,
  SpliceJunction = NULL,
  IntronCounts = NULL,
  SpliceFeature = NULL,
  SpliceFeatureValidated = NULL,
  PSI = NULL,
  GeneFeature = NULL,
  Exp = NULL,
  GTF = NULL
)

Arguments

SplicePheno

Data frame. Sample metadata.

SpliceJunction

Data frame. Splice junction counts matrix.

IntronCounts

Data frame. Intron coverage matrix.

SpliceFeature

List of data frames. Each data frame is the exon-level alternative splicing event metadata.

SpliceFeatureValidated

List of data frames. Each data frame is the validated (high-quality) exon-level alternative splicing event metadata.

PSI

Data frame. PSI matrix.

GeneFeature

Data frame. Gene metadata.

Exp

Data frame. Normalised, non-log2-transformed gene expression matrix.

GTF

Data frame. GTF used for generating the exon-level alternative splicing event metadata.

Value

An object of class S3.

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

SpliceJunction <- marvel.demo$SpliceJunction
SpliceJunction[1:5,1:5]

SplicePheno <- marvel.demo$SplicePheno
SplicePheno[1:5,]

SpliceFeature <- marvel.demo$SpliceFeature
SpliceFeature[["SE"]][1:5, ]

IntronCounts <- marvel.demo$IntronCounts
IntronCounts[1:5,1:5]

GeneFeature <- marvel.demo$GeneFeature
GeneFeature[1:5, ]

Exp <- marvel.demo$Exp
Exp[1:5,1:5]

marvel <- CreateMarvelObject(SpliceJunction=SpliceJunction,
                             SplicePheno=SplicePheno,
                             SpliceFeature=SpliceFeature,
                             IntronCounts=IntronCounts,
                             GeneFeature=GeneFeature,
                             Exp=Exp
                             )
class(marvel)