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

Description Usage Arguments Value Note Author(s) Examples

View source: R/msa.R

Description

Split an MSA by feature

Usage

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## 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

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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)

Example output



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