PlotPSI.SE.Pos: Plot percent spliced-in (PSI) values for skipped-exon (SE)...

In wenweixiong/VALERIE: Visualising Splicing at Single-Cell Resolution

Plot percent spliced-in (PSI) values for skipped-exon (SE) located on positive strand

Description

PlotPSI.SE.Pos computes percent spliced-in (PSI) at each genomic coordinate for skipped-exon (SE) located on positive (forward) strand.

Usage

PlotPSI.SE.Pos(
  tran_id,
  Bam,
  BamPheno,
  cell.types,
  min.coverage,
  cons.exon.cutoff,
  method,
  method.adj,
  sig.pval = 0.1,
  cell.types.colors,
  plot.title,
  plot.width,
  plot.height,
  plot.out,
  track = TRUE,
  nboots = 2000,
  show.mean.ci = TRUE
)

Arguments

tran_id	Character string. Splicing event nomenclature.
Bam	Character string. Path to folder where the BAM files and their corresponding index files are located.
BamPheno	object of class data.frame. Mandatory columns are bam.file.name and cell.type. bam.file.name column indicates BAM file names as per that found in the Bam folder. cell.type column indicates the cell group names.
cell.types	Character string. Cell types to plot. Should be the same number of cell groups or less than the cell.type column of the BamPheno argument.
min.coverage	Numeric value. Coverage (Total reads) threshold below which the PSI value of the genomic coordinate is annotate as missing value, i.e. no coverage.
cons.exon.cutoff	Numeric value. Limit the number of bases to plot for the constitutive exons. This allow users to focus the plots on the alternative exon.
method	Character string. Statistical test to compare the PSI values across the different cell types. "wilcox", "t.test", "ks", "ad", and "dts" available for 2-group comparison. "ANOVA" and "kw" available for 3- or more group comparison. "ks", "ad", "dts", and "kw", represent Kolmogorov–Smirnov, Anderson-Darling, DTS, and Kruskal-Wallis test, respectively.
method.adj	Character string. Adjust p-values for multiple testing. Options available as per p.adjust function.
sig.pval	Numeric value. Adjust p-value, below which, the p-value is considered statistically significant.
cell.types.colors	Character string. Legend colors for each cell type. Should be of same length as cell.types argument. To use ggplot2 default color scheme, please specify "ggplot.default".
plot.title	Character string. Main title for plot. Examples are gene ID, gene names, splicing ID etc..
plot.width	Numeric value. Width of plot.
plot.height	Numeric value. Height of plot.
plot.out	Character string. Path to folder to output plot.
track	Logical. If set to TRUE (default), a process of reading in the BAM files, which is the rate-limiting step, will be tracked on the console.
nboots	Numeric value. When method set to "dts", the number of bootstrap iterations for computing the p-value.
show.mean.ci	Logical value. If set to TRUE, the 95percent confidence interval of the per-cell group mean PSI values will not be shown. Default is FALSE.

Details

This function computes percent spliced-in (PSI) at each genomic coordinate for skipped-exon (SE) located on positive (forward) strand. Formula for computing PSI is number of reads with non-N CIGAR operation divided by the total number of reads. Total number of reads is the sum of reads with non-N CIGAR operation and reads with N-CIGAR operation

Value

A plot in PDF format located in the folder specified by plot.out argument.

Author(s)

Sean Wen <[e-mail]>

Examples

# Read sample metadata
path_to_file <- system.file("extdata", "BAM_PhenoData_Small.txt", package="VALERIE")
BamPheno <- read.table(path_to_file, sep="\t", header=TRUE, stringsAsFactors=FALSE)
head(BamPheno)

# Plot
PlotPSI.SE.Pos(
 tran_id="chr18:82554580:82554750:+@chr18:82561778:82561855:+@chr18:82572825:82572926",
 Bam=system.file("extdata/BAM", package="VALERIE"),
 BamPheno=BamPheno,
 cell.types=c("Ctrl", "EAE"),
 min.coverage=10,
 cons.exon.cutoff=100,
 method="t.test",
 method.adj="bonferroni",
 cell.types.colors="ggplot.default",
 plot.title="Mbp",
 plot.width=5,
 plot.height=8,
 plot.out=paste(tempdir(), "Plot.pdf", sep="")
 )

wenweixiong/VALERIE documentation built on Dec. 7, 2022, 4:15 a.m.