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inst/examples/split-by-feature-msa.R
In rphast: Interface to 'PHAST' Software for Comparative Genomics
require("rphast")
exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
files <- c("ENr334-100k.maf", "gencode.ENr334-100k.gff")
unzip(exampleArchive, files)
m <- read.msa("ENr334-100k.maf")
feats <- read.feat("gencode.ENr334-100k.gff")
feats$seqname <- "hg18"
cdsAlign <- split.by.feature.msa(m, feats[feats$feature=="CDS",])
unlink(files)
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rphast documentation built on May 1, 2019, 9:26 p.m.
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require("rphast")
exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
files <- c("ENr334-100k.maf", "gencode.ENr334-100k.gff")
unzip(exampleArchive, files)
m <- read.msa("ENr334-100k.maf")
feats <- read.feat("gencode.ENr334-100k.gff")
feats$seqname <- "hg18"
cdsAlign <- split.by.feature.msa(m, feats[feats$feature=="CDS",])
unlink(files)
Try the rphast package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
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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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