rphast (version 1.6.9)

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

# NOT RUN {
exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
files <- c("ENr334-100k.maf", "ENr334-100k.fa", "gencode.ENr334-100k.gff")
unzip(exampleArchive, files)
f <- read.feat("gencode.ENr334-100k.gff")
f$seqname <- "hg18.chr6"
m1 <- read.msa("ENr334-100k.maf", features=f, do.4d=TRUE)
m2 <- read.msa("ENr334-100k.maf")
m3 <- get4d.msa(m2, features=f)
m4 <- get4d.msa(read.msa("ENr334-100k.maf"), features=f)
m5 <- get4d.msa(read.msa("ENr334-100k.fa", offset=41405894), features=f)
unlink(files)
# }