DJEprepare: DJEprepare: Filtering junctions for differential expression...

In MauerLab/DJExpress: An integrated application for differential splicing analysis and visualization

Description

Filter junctions based on their expression. Returns output object for DJEanalize

Usage

DJEprepare(
  annotate.out,
  Group1,
  minMean = 10,
  maxMean = Inf,
  minVar = 0,
  maxVar = Inf
)

Arguments

annotate.out	output object from DJEannotate()
Group1	vector or factor specifying sample names in the control group
minMean	numeric: minimum of read count mean per junction
maxMean	numeric: maximum of read count mean per junction
minVar	numeric: minimum of read count variance per junction
maxVar	numeric: maximum of read count variance per junction

Value

List object containing expression-based filtered junction counts, gene annotation and design matrix for differential expression analysis

Examples

DJEann <- system.file("extdata", "DJEann.rds", package = "DJExpress")
ann.out <- readRDS(DJEann)
Group1 <- colnames(ann.out$quant.annotated)[grep("GTEx", colnames(ann.out$quant.annotated))]
prep.out <- DJEprepare(ann.out, Group1)

MauerLab/DJExpress documentation built on Jan. 1, 2022, 12:57 p.m.