plot_profile-methods: plot_profile method

In welch16/Segvis: Segvis: A package for visualization of high throughput sequencing data along genomic segments

Description

plot_profile return a ggplot2 object with the plot of the summarized functional profiles (summarized by using the argument FUN). For each coverage, file and distance from the anchor coordinate it applies FUN to the tags vector for all regions.

Usage

plot_profile(object, ...)

## S4 method for signature 'SegvisData'
plot_profile(object, FUN = mean,
  nameFiles = basename(files(object)), type = "aggr", base = 1e+06,
  mc.cores = getOption("mc.cores", 2L), ...)

Arguments

object	a SegvisData object.
...	Any other additional parameters that plot_profile may need.
FUN	a function to summarize the profiles by coordinate. The default value is the mean.
nameFiles	a character vector with the shortened names that are going to be used in the plot.
type	a character value indicating which strand to use. By default uses the aggregate coverage between both strands.
base	a numeric value indicating the number of aligned reads to which the signal is going to be normalized. The default value is 1e6. DT_profile always normalizes the signal.
mc.cores	a numeric value indicating the number of multi-cores to be used.

Value

The plot_profile method returns a ggplot2 object with the summarized functional profiles.

See Also

SegvisData-class

welch16/Segvis documentation built on May 4, 2019, 4:18 a.m.