frameCounting: Counts aligned reads within coding sequence regions by frame...

In riboSeqR: Analysis of sequencing data from ribosome profiling experiments

Description

Ribosome footprint sequencing reads aligning within coding sequence regions may align in the same frame (relative to start codon) as the coding sequence, or frame shifted by 1 or 2 frames. This function calls the number of aligning reads within the coding sequence, split by frame and footprint size.

Usage

frameCounting(riboDat, cds, lengths = 25:30, offset5p = 0, offset3p = 0)

Arguments

riboDat	A riboData object containing the ribosome footprints to be counted.
cds	A GenomicRanges object containing the coordinates of the coding sequences.
lengths	Lengths of ribosome footprints to be included in the riboData object.
offset5p	An offset to the 5' end of the coding sequence coordinates to include ribosome footprints some distance upstream of coding start.
offset3p	An offset to the 3' end of the coding sequence coordinates to exclude reads too close to coding stop.

Value

A riboCoding object.

Author(s)

Thomas J. Hardcastle

See Also

riboData

Examples

#ribosomal footprint data
datadir <- system.file("extdata", package = "riboSeqR")
ribofiles <- paste(datadir, 
                   "/chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "")
rnafiles <- paste(datadir, 
                  "/chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "")

riboDat <- readRibodata(ribofiles, rnafiles, replicates = c("WT", "WT",
"M", "M"))

# CDS coordinates
chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "")
fastaCDS <- findCDS(fastaFile = chlamyFasta, 
                    startCodon = c("ATG"), 
                    stopCodon = c("TAG", "TAA", "TGA"))

# frame calling
fCs <- frameCounting(riboDat, fastaCDS)

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