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

In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description

Split an MSA by feature

Usage

## S3 method for class '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

Note

Neither x nor f will be altered by this function if they are stored as pointers.

Author(s)

Melissa J. Hubisz and Adam Siepel

Examples

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)

Example output

rphast documentation built on May 1, 2019, 9:26 p.m.