print_period_region_length: print_period_region_length

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

print_period_region_length

Description

Function to print out periodicity by length and region plots of all samples to a pdf file

Usage

print_period_region_length(reads_psite_list, outfile, cl = 95)

Arguments

reads_psite_list	A reads_psite_list object produced by psite_info_rW
outfile	The path and name of the output pdf file
cl	An integer in [1,100] specifying a confidence level to restrict the plot to a sub-range of read lengths. Use this argument to avoid printing out uncommon read lengths. Default:95.

Details

These plots illustrate the 3-base (reading-frame-dependent) periodicity of reads, separately for 5'UTR, CDS and 3'UTR and stratified by read length. They can inform the choice of read length range for further analysis of ribo-seq data. Good-length reads are abundant and show enrichment for frame 1 in the CDS region.

Examples

print_period_region_length(reads_psite_list, "<file.path>/Periodicity_by_length_region2.pdf")

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