DT_region-methods: DT_region method

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

Description

DT_region returns a data.table with the info. necessary to plot the coverage of the aligned read files across the peak_idth element of the SegvisData object.

Usage

DT_region(object, region, ...)

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

## S4 method for signature 'SegvisData,numeric'
DT_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 or a GRanges object indicating a whole region to plot.
...	Any other additional parameters that DT_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 DT_region method returns a data.table object with the info. necessary to be plotted.

See Also

SegvisData-class

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