findCDS: Parses a transcriptome file looking for start/stop codons in...

In riboSeqR: Analysis of sequencing data from ribosome profiling experiments

Description

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.

Usage

findCDS(fastaFile, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA"))

Arguments

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").

Value

A GRanges object.

Author(s)

Thomas J. Hardcastle

Examples

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"))

Example output

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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riboSeqR documentation built on Nov. 8, 2020, 8:23 p.m.