PctASE: Tabulate differentially spliced splicing event

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

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"
)

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.

Value

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

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
                      )

MARVEL documentation built on Oct. 31, 2022, 5:07 p.m.