rnaCounts: Extracts mRNA counts from a riboDat object for a set of...

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/sliceCounts.R

Description

Takes mRNA count data from riboDat object, maps them to coding sequences specified in GRanges object, and counts the total number of hits. This is a crude approach intended to quickly produce comparable data to ribosome footprint counts. More sophisticated alternatives, addressing coverage variation, isoforms, multireads &c. have been widely described in the literature on mRNA-seq analyses.

Usage

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rnaCounts(riboDat, CDS)

Arguments

riboDat

A riboData object containing the RNA-seq alignments.

CDS

A GRanges object defining the coordinates of the coding sequences for which to acquire counts.

Details

The count data thus acquired can be compared to counts of ribosomal footprint data through a beta-binomial analysis (see vignette) to discover differential translation.

Value

A matrix containing count data for the RNA-seq libraries.

Author(s)

Thomas J. Hardcastle

See Also

sliceCounts

Examples

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#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)

# analysis of frame shift for 27 and 28-mers.
fS <- readingFrame(rC = fCs, lengths = 27:28)

# filter coding sequences. 27-mers are principally in the 1-frame,
# 28-mers are principally in the 0-frame relative to coding start (see
# readingFrame function).

ffCs <- filterHits(fCs, lengths = c(27, 28), frames = list(1, 0), 
                   hitMean = 50, unqhitMean = 10, fS = fS)

# Extract counts of RNA hits from riboCount data.
rnaCounts <- rnaCounts(riboDat, ffCs@CDS)

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