inst/examples/get4d-msa.R

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

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)