profilePlots {Repitools} | R Documentation

## 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.

[Package Repitools version 1.30.0 Index]