psite_to_codon_count: psite_to_codon_count

In goodarzilab/Ribolog: Logistic-regression-based analysis of ribosome profiling data

psite_to_codon_count

Description

Function to count reads per codon for each transcript.

Usage

psite_to_codon_count(reads_psite_list, length_range, annotation,
  fasta.file)

Arguments

reads_psite_list	A reads_psite_list object produced by psite_info_rW
length_range	Range of read lengths to be included in calculation of per codon RPF counts. Longer and shorter reads may be excluded because of high uncertainty in offset assignment, lack of expected periodicity, etc.
annotation	Annotation data table produced by read_annotation listing transcript names and lengths of their 5'UTR, CDS and 3'UTR segments. It has five columns: transcript, l_tr, l_utr5, l_cds and l_utr3. Transcript names and segment lengths must correspond to the reference sequences to which the reads were mapped.
fasta.file	The reference fasta file to which reads were mapped.

Value

A list of lists with the following structure: list$<sample.name>$<transcript.ID> data.frame: [1] codon_number [2] codon_type [3] aa_type [4] observed_count

Examples

tr_codon_read_count_LMCN <- psite_to_codon_count(reads_psite_list_LMCN, c(24:32), annotation_human_cDNA, "<file.path>/Human.GRC38.96_cDNA_longest_CDS.txt")

goodarzilab/Ribolog documentation built on Oct. 7, 2022, 10:14 p.m.