DetectEvents.AFE.NegStrand {MARVEL}

Detect alternative first exons on negative strand

Description

Detects alternative first exons, specifically for genes transcribed on the negative strand of the DNA.

Usage

DetectEvents.AFE.NegStrand(
  MarvelObject,
  parsed.gtf = NULL,
  min.cells = 50,
  min.expr = 1,
  track.progress = FALSE
)

Arguments

MarvelObject

S3 object generated from CreateMarvelObject function.

parsed.gtf

Data frame. GTF file with the gene_id parsed. Generated from the DetectEvents.AFE function.

min.cells

Numeric value. The minimum number of cells in which the gene is expressed for the gene to included for splicing event detected and quantification. To be used in conjunction with min.expr argument. Default value is 50.

min.expr

Numeric value. The minimum expression value for the gene to be considered to be expressed in a cell. Default value is 1.

track.progress

Logical. If set to TRUE, progress bar will appear to track the progress of the rate-limiting step of this function, which is the extraction of the final exon-exon junctions. Default value is FALSE.

Value

An object of class S3 with new slot MarvelObject$SpliceFeature$AFE.NegStrand.

Examples

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

marvel.demo <- DetectEvents.AFE.NegStrand(MarvelObject=marvel.demo,
                                          parsed.gtf=NULL,
                                          min.cells=5,
                                          min.expr=1,
                                          track.progress=FALSE
                                          )