print_read_end_heatmap: print_read_end_heatmap

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

print_read_end_heatmap

Description

Function to print out metaheatmaps of reads around start and stop codons for all samples to a pdf file.

Usage

print_read_end_heatmap(reads_list, annotation, outfile, cl = 85,
  utr5l = 50, cdsl = 50, utr3l = 50)

Arguments

reads_list	A reads_list object produced by bamtolist_rW
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.
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:85.
utr5l	Length of 5'UTR segment to be included upstream of translation start site. Default: 50.
cdsl	Length of coding sequence to be included downstream of translation start site and upstream of translation termination site. Default: 50.
utr3l	Length of 3'UTR segment to be included downstream of translation termination site. Default: 50.

Details

Heatmaps of reads (stratified by read length) mapping to positions around the start and stop codon provide a visual sense regarding a reasonable offset for p-site assignment as well as the 3-base periodicity of RPF reads.

Examples

print_read_end_heatmap(reads_list_LMCN, annotation_human_cDNA, "<file.path>/LMCN_RPF_read_end_heatmaps.pdf")

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