chromosomeMappingSummary: prepare mapping summary information by chromosome
In sagrudd/nanopoRe: Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data
Description
Usage
Arguments
Value
Examples
View source: R/ReferenceGenome.R
Description
This method will return a data.frame of basic per chromosome mapping
statistics
Usage
1
chromosomeMappingSummary(chrIds, bamFile, flag = "Primary")
Arguments
chrIds
vector of chromosome ids
bamFile
to the bamFile used for analysis
flag
to define whether mapping is reported at the Primary level
Value
data.frame of mapping characteristics
Examples
1
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5
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8
9
init()
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)
chromosomeMappingSummary(getChromosomeIds(), demoBam)
sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.
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Description Usage Arguments Value Examples
View source: R/ReferenceGenome.R
Description
This method will return a data.frame of basic per chromosome mapping statistics
Usage
1 | chromosomeMappingSummary(chrIds, bamFile, flag = "Primary")
|
Arguments
chrIds |
vector of chromosome ids |
bamFile |
to the bamFile used for analysis |
flag |
to define whether mapping is reported at the Primary level |
Value
data.frame of mapping characteristics
Examples
1 2 3 4 5 6 7 8 9 | init()
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)
chromosomeMappingSummary(getChromosomeIds(), demoBam)
|
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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