profilePlots: Create line plots of averaged signal across a promoter for...

In markrobinsonuzh/Repitools: Epigenomic tools

Create line plots of averaged signal across a promoter for gene sets, compared to random sampling.

Description

Creates a plot where the average signal across a promoter of supplied gene lists is compared to random samplings of all genes, with a shaded confidence area.

Usage

  ## S4 method for signature 'ScoresList'
profilePlots(x, summarize = c("mean", "median"), gene.lists,
   n.samples = 1000, confidence = 0.975, legend.plot = "topleft", cols = rainbow(length(gene.lists)),
   verbose = TRUE, ...)

Arguments

x	A ScoresList object. See featureScores.
summarize	How to summarise the scores for each bin into a single value.
gene.lists	Named list of logical or integer vectors, specifying the genes to be averaged and plotted. NAs are allowed if the vector is logical.
n.samples	The number of times to randomly sample from all genes.
confidence	A percentage confidence interval to be plotted (must be > 0.5 and < 1.0).
legend.plot	Where to plot the legend - directly passed to legend. NA suppresses the legend.
cols	The colour for each of the genelists supplied.
verbose	Whether to print details of processing.
...	Extra arguments to matplot, like x- and y-limits, perhaps.

Details

For each table of scores in x, a plot is created showing the average signal of the genes specified in each list element of gene.lists compared to n.samples random samplings of all genes, with confidence % intervals shaded. If an element of gene.lists is a logical vector, its length must be the same as the number of rows of the score tables.

Value

A series of plots.

Author(s)

Aaron Statham

Examples

  # See examples in manual.

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.