codonInfo {RiboProfiling} | R Documentation |
Associates the read counts on codons with the codon type for each ORF.
codonInfo(listReadsCodon, genomeSeq, orfCoord, motifSize)
listReadsCodon |
a list of data.frame objects. It contains the number of reads per codon in a CDS. |
genomeSeq |
a BSgenome object. It contains the full genome sequences for the organism. |
orfCoord |
a GRangesList. The coordinates of the ORFs on the genome. |
motifSize |
an integer. The number of nucleotides in each motif on which to compute coverage and usage. Either 3, 6, or 9. Default 3 nucleotides (codon). Attention! For long motifs, the function can be quite slow!! |
a list of 2 data.frame objects: one with the number of times each codon type is found in each ORF and one with the number of reads for each codon type in each ORF.
#for each codon in each ORF get the read coverage #parameter listReadsCodon can be returned by the riboSeqFromBam function #it corresponts to the 2nd element in the list returned by riboSeqFromBam data(codonIndexCovCtrl) listReadsCodon <- codonIndexCovCtrl txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene #get the names of the ORFs #grouped by transcript cds <- GenomicFeatures::cdsBy(txdb, use.names=TRUE) orfCoord <- cds[names(cds) %in% names(listReadsCodon)] #get the genome, please check that the genome has the same seqlevels genomeSeq <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 #if not rename it #gSeq <- GenomeInfoDb::renameSeqlevels(genomeSeq, #sub("chr", "", GenomeInfoDb::seqlevels(genomeSeq))) #codon frequency, coverage, and annotation codonData <- codonInfo(listReadsCodon, genomeSeq, orfCoord)