coverage.rpm: Coverage calculation and normalization to reads per million...

In gthar/nucleR: Nucleosome positioning package for R

Description

Calculates the coverage values from a GenomicRanges::GRanges or IRanges::IRanges object normalized to reads per million, allowing the comparison of experiments with a different absolut number of reads.

Usage

coverage.rpm(data, scale = 1e+06, ...)

## S4 method for signature 'GRanges'
coverage.rpm(data, scale = 1e+06, ...)

## S4 method for signature 'CompressedGRangesList'
coverage.rpm(data, scale = 1e+06, ...)

## S4 method for signature 'IRanges'
coverage.rpm(data, scale = 1e+06, ...)

## S4 method for signature 'RangedData'
coverage.rpm(data, scale = 1e+06, ...)

Arguments

data	GenomicRanges::GenomicRanges or IRanges::IRanges with the reads information
scale	By default, a million (1e6), but you could change this value for abnormal high or low amount of reads.
...	Additional arguments to be passed to coverage function

Value

RleList object with the coverage objects

Author(s)

Oscar Flores [e-mail]

See Also

processReads(), IRanges::coverage()

Examples

# Load the example dataset and get the coverage
data(nucleosome_htseq)
cov <- coverage.rpm(nucleosome_htseq)
print(cov)
# Plot it
library(ggplot2)
cover <- as.vector(cov[["chr1"]])
qplot(seq_along(cover), cover, geom="line", ylab="coverage",
  xlab="position")

gthar/nucleR documentation built on May 28, 2019, 4:37 p.m.