plot_region-methods: plot_region method

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

Description

plot_region plots the coverage of the aligned read files across the peak_idth element of the SegvisData object.

Usage

plot_region(object, region, ...)

## S4 method for signature 'SegvisData,GRanges'
plot_region(object, region,
  nameFiles = basename(files(object)), type = "aggr", normalize = TRUE,
  base = 1e+06)

## S4 method for signature 'SegvisData,numeric'
plot_region(object, region,
  nameFiles = basename(files(object)), type = "aggr", normalize = TRUE,
  base = 1e+06)

Arguments

object	a SegvisData object.
region	a numeric value indicating which region to plot in the SegvisData object or a GRanges object with a genomic region that is not recorded in the SegvisData object
...	Any other additional parameters that plot_region may need.
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.
normalize	a logical value indicating if the profiles are normalized respect to its number of reads.
base	a numeric value indicating the number of aligned reads to which the signal is going to be normalized. The default value is 1e6.

Value

The plot_region method returns a ggplot object with the desired plot.

See Also

SegvisData-class

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