plotOverallCovHistogram: plot a histogram of whole genome depth-of-coverage
In sagrudd/nanopoRe: Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data
Description
Usage
Arguments
Value
Examples
View source: R/PlotsDepthOfCoverage.R
Description
This method will plot a histogram of whole genome depth-of-coverage
Usage
1
plotOverallCovHistogram(bamFile = NULL, segments = 50, ...)
Arguments
bamFile
is the path to the bamFile to plot
segments
number of segments to split data into
...
such as FORCE=TRUE
Value
ggplot2 plot
Examples
1
2
3
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5
6
7
8
9
demoBam <- system.file("extdata",
"Ecoli_zymo_R10_filt_subs.bam",
package = "nanopoRe")
referenceFasta <- system.file("extdata",
"Escherichia_coli_complete_genome.fasta",
package = "nanopoRe")
setReferenceGenome(referenceFasta)
bamSummarise(demoBam, blockSize=1000L)
plotOverallCovHistogram()
sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.
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Description Usage Arguments Value Examples
View source: R/PlotsDepthOfCoverage.R
Description
This method will plot a histogram of whole genome depth-of-coverage
Usage
1 | plotOverallCovHistogram(bamFile = NULL, segments = 50, ...)
|
Arguments
bamFile |
is the path to the bamFile to plot |
segments |
number of segments to split data into |
... |
such as FORCE=TRUE |
Value
ggplot2 plot
Examples
1 2 3 4 5 6 7 8 9 | demoBam <- system.file("extdata",
"Ecoli_zymo_R10_filt_subs.bam",
package = "nanopoRe")
referenceFasta <- system.file("extdata",
"Escherichia_coli_complete_genome.fasta",
package = "nanopoRe")
setReferenceGenome(referenceFasta)
bamSummarise(demoBam, blockSize=1000L)
plotOverallCovHistogram()
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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