Skip to content

Instantly share code, notes, and snippets.

@mtmorgan
Last active September 20, 2017 09:41
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save mtmorgan/dcbd861c55cec573ff07533e3c8386b2 to your computer and use it in GitHub Desktop.
Save mtmorgan/dcbd861c55cec573ff07533e3c8386b2 to your computer and use it in GitHub Desktop.
dna <- getFastaSeq()
## function for finding orfs. Returned as IRanges.
ORFdef <- find_in_frame_ORFs(dna, longestORF = FALSE, minimumLength = 8)
ORFdef <- ORFdef[lengths(ORFdef) > 0]
## Map (mapply) on each five prime leader
uORFs <- Map(
function(granges, tx_name, ORFdef) {
map_granges(ORFdef, granges, tx_name)
},
fiveUTRs, names(fiveUTRs),
MoreArgs=list(ORFdef = ORFdef)
)
## ?? not sure what map_granges returns
## uORFs <- GRangesList(unlist(uORFs))
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment