MARVEL (version 1.4.0)

CreateMarvelObject: 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
)

Value

An object of class S3.

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.

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)