cds_coverage: Number of in-frame P-sites per coding sequence or transcript.

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

Number of in-frame P-sites per coding sequence or transcript.

Description

This function generates a data table that for each transcript contains at least i) its name; ii) its length or the length of its annotated coding sequence (if any); iii) the number of P-sites falling in its annotated coding sequence or in the whole transcript for all samples. When the coverage is computed for coding sequences and not whole transcripts, a chosen number of nucleotides at the beginning and/or at the end of the CDSs can be excluded for restricting the analysis to a portion of the original coding sequence. In this case the output data table includes an additional column reporting the length of the selected region. Moreover, either all P-sites or only in-frame P-sites can be considered. Finally, transcripts without annotated CDS are automatically discarded.

Usage

cds_coverage(
  data,
  annotation,
  start_nts = 0,
  stop_nts = 0,
  in_frame = TRUE,
  whole_transcript = FALSE
)

Arguments

data	Either list of data tables or GRangesList object from psite_info.
annotation	Data table as generated by create_annotation.
start_nts	Positive integer specifying the number of nucleotides at the beginning of the coding sequences to be excluded from the analisys. Default is 0. This parameter is considered only if whole_transcript is FALSE.
stop_nts	Positive integer specifying the number of nucleotides at the end of the coding sequences to be excluded from the analisys. Default is 0. This parameter is considered only if whole_transcript is FALSE.
in_frame	Logical value whether to consider only in-frame P-sites when computing the coverage. Default is TRUE. This parameter is considered only if whole_transcript is FALSE.
whole_transcript	Logical value whether to compute the coverage based on P-sites falling in any region of the transcript, i.e. CDS and UTRs. Default is FALSE.

Value

A data table.

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 number of in-frame P-sites per whole coding sequences.
## psite_cds <- cds_coverage(reads_psite_list, mm81cdna)
## 
## ## Compute the number of in-frame P-sites per coding sequences exluding
## ## the first 15 nucleotides and the last 10 nucleotides.
## psite_cds <- cds_coverage(reads_psite_list, mm81cdna,
##                           start_nts = 15, stop_nts = 10)
## 
## ## Compute the number of P-sites per transcripts.
## psite_cds <- cds_coverage(reads_psite_list, mm81cdna,
##                           whole_transcript = TRUE)

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