rends_heat_rW: rends_heat_rW

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

rends_heat_rW

Description

Function to print out read end heatmaps of a sample.

Usage

rends_heat_rW(reads_list, annotation, sample, transcripts = NULL,
  cl = 95, utr5l = 50, cdsl = 50, utr3l = 50, log_colour = F,
  colour = "black")

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.
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.
outfile	The path and name of the output pdf file.

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.