Description Usage Arguments Value Author(s) Examples
Looks in the fastaFile for defined start and stop codons in frame with one another. Reports the discovered coordinates as a GRanges object with a ‘frame’ value.
1 |
fastaFile |
Fasta file of transcriptome sequences. |
startCodon |
Vector of possible start codons. Defaults to "ATG". |
stopCodon |
Vector of possible stop codons. Defaults to c("TAG", "TAA", "TGA"). |
A GRanges object.
Thomas J. Hardcastle
1 2 3 4 5 | datadir <- system.file("extdata", package = "riboSeqR")
chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "")
fastaCDS <- findCDS(fastaFile = chlamyFasta,
startCodon = c("ATG"),
stopCodon = c("TAG", "TAA", "TGA"))
|
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: abind
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