rphast (version 1.6.9)

split.by.feature.msa: Split an MSA by feature

Description

Split an MSA by feature

Usage

# S3 method for by.feature.msa
split(x, f, drop = FALSE, pointer.only = FALSE,
  ...)

Arguments

x

An object of type msa

f

An object of type feat

drop

Not currently used

pointer.only

If TRUE, returned list elements are pointers to objects stored in C (advanced use only).

...

Not currently used

Value

A list of msa objects, representing the sub-alignments for each element in f

Examples

# NOT RUN {
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)
# }