profilePlots: Create line plots of averaged signal across a promoter for...
In Repitools: Epigenomic tools

Description Usage Arguments Details Value Author(s) Examples

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.

  ## 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, ...)

`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.

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.

A series of plots.

Aaron Statham