create_te: create_te

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

create_te

Description

Function to create a TE (translational efficiency) data frame from a combined RNA+RPF data frame.

Usage

create_te(x, idcolumns = NULL, rnacolumns, rpfcolumns)

Arguments

x	Input data frame containing RNA-seq or Ribo-seq data. Rows are genes/transcripts and columns are samples. The data.frame may contain additional columns for gene/transcript ID or other metadata.
idcolumns	A vector specifying the columns to be excluded from the calculations. These columns may contain the gene/transcript ID or any metadata that need to be preserved.
rnacolumns	A vector specifying the columns containing RNA counts
rpfcolumns	A vector specifying the columns containing RPF counts

Details

Translational efficiency is calculated as RPF/RNA. The number and order of samples must be the same in RNA and RPF columns.

Value

A data frame containing the original ID columns and the calculated TE columns.

Examples

te_LMCN <- create_te(rr_LMCN.v2, 1, c(2:9), c(10:17))

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