frame_psite_rW: frame_psite_rW

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

frame_psite_rW

Description

Function to plot the percentage of psites falling into each of the three reading frames (periodicity)

Usage

frame_psite_rW(reads_psite_list, sample = NULL, transcripts = NULL,
  region = "all", length_range = "all", plot_title = NULL)

Arguments

reads_psite_list	A reads_psite_list object produced by psite_info_rW
sample	Sample to be plotted.
transcripts	Vector of transcript names to be included. Default: NULL (includes all transcripts).
region	"5utr", "cds", "3utr" or "all". Default: "all".
length_range	Range of read lengths to be included. Default: "all".
plot_title	Title of the plot. Default: NULL.

Details

This function produces bar plots of the percentage of psites falling into each of the three possible reading frames, separately for 5' UTR, CDS and 3' UTR regions. In a good dataset, psites in CDS should be enriched for frame 1.

Examples

frame_psite_rW(reads_psite_list_LMCN, "CN34_r2_rpf")

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