codon_coverage: Number of reads per codon.

In LabTranslationalArchitectomics/riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

Number of reads per codon.

Description

This function computes transcript-specific codon coverages, defined as the number of either read footprints or P-sites mapping on each triplet of coding sequences and UTRs (see Details). The resulting data table contains, for each triplet: i) the name of the corresponding reference sequence (i.e. of the transcript to which it belongs); ii) its leftmost and rightmost position with respect to the 1st nucleotide of the reference sequence; iii) its position with respect to the 1st and the last codon of the annotated CDS of the reference sequence; iv) the region of the transcript (5' UTR, CDS, 3' UTR) it is in; v) the number of read footprints or P-sites falling in that region for all samples.

Usage

codon_coverage(
  data,
  annotation,
  sample = NULL,
  psite = FALSE,
  min_overlap = 1,
  output_class = "datatable"
)

Arguments

data	Either list of data tables or GRangesList object from psite_info. Data tables and GRanges objects generated by bamtolist and bedtolist can be used if psite is FALSE (the default).
annotation	Data table as generated by create_annotation.
sample	Character string vector specifying the name of the sample(s) of interest. Default is NULL i.e. all samples in data are processed.
psite	Logical value whether to return the number of P-sites per codon. Default is TRUE. If FALSE, the number of read footprints per codon is returned instead.
min_overlap	Positive integer specifying the minimum number of overlapping positions (in nucleotides) between reads and codons to be considered overlapping. If psite is TRUE this parameter must be 1 (the default).
output_class	Either "datatable" or "granges". It specifies the format of the output i.e. a list of data tables or a GRangesList object. Default is "datatable".

Details

The sequence of every transcript is divided in triplets starting from the annotated translation initiation site (if any) and proceeding towards the UTRs extremities, possibly discarding the exceeding 1 or 2 nucleotides at the extremities of the transcript. Please note: transcripts not associated to any annotated 5' UTR, CDS and 3'UTR and transcripts whose coding sequence length is not divisible by 3 are automatically discarded.

Value

A data table or GRanges object.

Examples

## data(reads_list)
## data(mm81cdna)
##
## ## compute and add p-site datails
## psite_offset <- psite(reads_list, flanking = 6, extremity = "auto")
## reads_psite_list <- psite_info(reads_list, psite_offset)
##
## Compute the codon coverage based on the number of ribosome footprint per
## codon, setting the minimum overlap between reads and triplets to 3 nts:
## coverage_dt <- codon_coverage(reads_psite_list, mm81cdna, min_overlap = 3)
## 
## Compute the coverage based on the number of P-sites per codon:
## coverage_dt <- codon_coverage(reads_psite_list, mm81cdna, psite = TRUE)

LabTranslationalArchitectomics/riboWaltz documentation built on Jan. 17, 2024, 12:18 p.m.