MARVEL (version 1.4.0)

PctASE: Tabulate differentially spliced splicing event

Description

Tabulates the percentage or absoluate number of significant splicing events for each splicing type.

Usage

PctASE(
  MarvelObject,
  method,
  psi.pval,
  psi.mean.diff,
  ylabels.size = 8,
  barlabels.size = 3,
  x.offset = 0,
  direction.color = NULL,
  mode = "percentage"
)

Value

An object of class S3 with new slots MarvelObject$DE$AbsASE$Table and MarvelObject$DE$AbsASE$Plot.

Arguments

MarvelObject

Marvel object. S3 object generated from CompareValues function.

method

Character string. The statistical method used for differential splicing analysis.

psi.pval

Numeric value. Adjusted p-value below which the splicing event is considered differentially spliced and included for tabulation.

psi.mean.diff

Numeric value. The minimum absolute differences in PSI values between the two cell groups above which the splicing event is considered differentially spliced and included for tabulation.

ylabels.size

Numeric value. Size of the xtick labels. Default is 8.

barlabels.size

Numeric value. Size of the labels above each bar. Default is 3

x.offset

Numeric value. The values on the x-axis to offset by. Useful when right margin overshadow the numbers above the bars. Default value is 0.

direction.color

Character strings. Vector of length 2 to specify the colors for significanly down- and up-regulated splicing events. Default is NULL, which corresponds to default ggplot2 color scheme.

mode

Character strings. When set to "percentage" (default), percentage of significant splicing events over total splicing events detected will be tabulate. When set to absolute, the number of significant splicing events will be tabulated.

Examples

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

marvel.demo <- PctASE(MarvelObject=marvel.demo,
                      method="ad",
                      psi.pval=0.1,
                      psi.mean.diff=0
                      )