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

Description Usage Arguments Value Author(s) See Also Examples

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

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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 [email protected]

See Also

processReads(), IRanges::coverage()

Examples

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# 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")

nucleR documentation built on Nov. 1, 2018, 2:23 a.m.