R: Calculate coverage

stat_coverage {ggbio}

R Documentation

Calculate coverage

Description

Calculate coverage.

Usage

# for GRanges
## S4 method for signature 'GRanges'
stat_coverage(data, ..., xlim, xlab, ylab, main,
              facets = NULL, geom = NULL)
# for GRangesList
## S4 method for signature 'GRangesList'
stat_coverage(data, ..., xlim, xlab, ylab, main,
              facets = NULL, geom = NULL)

# for Bamfile
## S4 method for signature 'BamFile'
stat_coverage(data, ..., maxBinSize = 2^14,
               xlim, which, xlab, ylab,
               main, facets = NULL, geom = NULL,
               method = c("estimate", "raw"),
               space.skip = 0.1, coord = c("linear", "genome"))

Arguments

`data`	A `GRanges` or `data.frame` object.
`...`	Extra parameters such as aes() passed to `geom_rect`, `geom_alignment`, or `geom_segment`.
`xlim`	Limits for x.
`xlab`	Label for x
`ylab`	Label for y
`main`	Title for plot.
`facets`	Faceting formula to use.
`geom`	The geometric object to use display the data.
`maxBinSize`	maxBinSize.
`method`	'estimate' for parsing estimated coverage(fast), 'raw' is slow and parse the accurate coverage.
`which`	`GRanges` which defines region to subset the results.
`space.skip`	used for coordinate genome, skip between chromosomes.
`coord`	coordinate system.

Value

A 'Layer'.

Author(s)

Tengfei Yin

Examples

library(ggbio)
## ======================================================================
##  simmulated GRanges
## ======================================================================
set.seed(1)
N <- 1000
library(GenomicRanges)
gr <- GRanges(seqnames = 
              sample(c("chr1", "chr2", "chr3"),
                     size = N, replace = TRUE),
              IRanges(
                      start = sample(1:300, size = N, replace = TRUE),
                      width = sample(70:75, size = N,replace = TRUE)),
              strand = sample(c("+", "-", "*"), size = N, 
                replace = TRUE),
              value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
              sample = sample(c("Normal", "Tumor"), 
                size = N, replace = TRUE),
              pair = sample(letters, size = N, 
                replace = TRUE))
ggplot(gr) + stat_coverage()

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ggplot() + stat_coverage(gr)

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ggplot(gr) + stat_coverage(geom = "point")

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ggplot(gr) + stat_coverage(geom = "area")

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ggplot(gr) + stat_coverage(aes(y = ..coverage..), geom = "histogram")

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ggplot(gr) + stat_coverage(aes(y = ..coverage..)) + geom_point()

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## for bam file
## TBD

[Package ggbio version 1.5.20 ]