codon2transcript: codon2transcript

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

codon2transcript

Description

Function to sum up codon counts per transcript.

Usage

codon2transcript(tr_codon_read_count_loess_corrected_list, count_type)

Arguments

tr_codon_read_count_loess_corrected_list	A list of codon level read counts for all samples and transcripts. It is the second element of a tr_codon_bias_coeff_corrected_count object produced by CELP_bias. It has the following structure: list$<sample.name>$<transcript.ID> data.frame: [1] codon_number [2] codon_type [3] aa_type [4] observed_count [5] bias_coefficient [6] corrected_count.
count_type	Options: "observed_count", "corrected_count".

Details

Stalling bias correction is performed at the codon level but differential translational efficiency analysis is ususally performed at transcript level. This function sums up codon level counts (observed or corrected) for each transcript.

Value

A data frame where the first column is transcript IDs and the remaining columns contain per transcript read counts for all samples.

Examples

rpf_observed_sum_LMCN <- codon2transcript(tr_codon_bias_coeff_loess_corrected_count_LMCN$tr_codon_read_count_loess_corrected, "observed_count")
rpf_corrected_sum_LMCN <- codon2transcript(tr_codon_bias_coeff_loess_corrected_count_LMCN$tr_codon_read_count_loess_corrected, "corrected_count")

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