call_resistance: HSV Resistance Genotyping from command line
In ojcharles/hsvdrg: Herpes Simplex Virus 1 and 2 Drug Resistance Genotyping
Description
Usage
Arguments
Value
View source: R/call_resistance.R
Description
Command line version of the website application
Takes as input a VCF, varscan tab or fasta file.
The program assumes variant files are generated relative to Merlin strain.
Fasta files if not Whole Genome, or not aligned / assembled relative to Merlin
are Processed using MAFFT & snp-sites.
In this case the output files are returned to your working directory.
Usage
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call_resistance(
infile = system.file("testdata", "F716L.fasta", package = "hsvdrg"),
all_mutations = FALSE,
inc_anecdotal = FALSE,
outdir = ""
)
Arguments
infile
the input fasta, vcf or varscan.tab file
all_mutations
when FALSE only recognised resistant variants present are returned.
inc_anecdotal
include anectodat database entries in returned results?
outdir
for fasta input files intermediate alignment fasta & vcf files are generated, this defines the directory they are saved to. "out.fasta" "out.vcf"
Value
A data.frame containing resistance information for variants identified
ojcharles/hsvdrg documentation built on Jan. 19, 2021, 2:02 p.m.
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Description Usage Arguments Value
View source: R/call_resistance.R
Description
Command line version of the website application Takes as input a VCF, varscan tab or fasta file. The program assumes variant files are generated relative to Merlin strain. Fasta files if not Whole Genome, or not aligned / assembled relative to Merlin are Processed using MAFFT & snp-sites. In this case the output files are returned to your working directory.
Usage
1 2 3 4 5 6 | call_resistance(
infile = system.file("testdata", "F716L.fasta", package = "hsvdrg"),
all_mutations = FALSE,
inc_anecdotal = FALSE,
outdir = ""
)
|
Arguments
infile |
the input fasta, vcf or varscan.tab file |
all_mutations |
when FALSE only recognised resistant variants present are returned. |
inc_anecdotal |
include anectodat database entries in returned results? |
outdir |
for fasta input files intermediate alignment fasta & vcf files are generated, this defines the directory they are saved to. "out.fasta" "out.vcf" |
Value
A data.frame containing resistance information for variants identified
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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