rphast (version 1.0)

get4d.msa: Extract fourfold degenerate sites from an MSA object...

Description

Extract fourfold degenerate sites from an MSA object

Usage

get4d.msa(x, features)

Arguments

x

An object of type msa

features

an object of type feat. Should have defined coding regions with feature type "CDS"

Value

• an unordered msa object containing only the sites which are fourfold degenerate

Examples

require("rphast")
exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
files <- c("ENr334.maf", "ENr334.fa", "gencode.ENr334.gff")
unzip(exampleArchive, files)
f <- read.feat("gencode.ENr334.gff")
f$seqname <- "hg18.chr6"
m1 <- read.msa("ENr334.maf", features=f, do.4d=TRUE)
m2 <- read.msa("ENr334.maf")
m3 <- get4d.msa(m2, features=f)
m4 <- get4d.msa(read.msa("ENr334.maf"), features=f)
m5 <- get4d.msa(read.msa("ENr334.fa", offset=41405894), features=f)
unlink(files)