Description Usage Arguments Value Note Author(s) Examples
Extract fourfold degenerate sites from an MSA object
1 | get4d.msa(x, features)
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x |
An object of type |
features |
an object of type |
An unordered msa object containing only the sites which are fourfold degenerate.
If x is stored as a pointer, it will be reduced to four-fold degenerate sites, so the original alignment will be lost. Use get4d.msa(copy.msa(x), features) to avoid this behavior. The return value will always be stored in R regardless of how the original alignment was stored.
For very large MSA objects it is more efficient to use the do.4d option in the read.msa function instead.
Melissa J. Hubisz and Adam Siepel
1 2 3 4 5 6 7 8 9 10 11 | 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)
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