metaprofile_psite_rW: metaprofile_psite_rW

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

metaprofile_psite_rW

Description

Function to plot read metaprofiles around the start and stop codons for a sample

Usage

metaprofile_psite_rW(reads_psite_list, annotation, sample,
  scale_factors = NULL, length_range = "all", transcripts = NULL,
  utr5l = 25, cdsl = 50, utr3l = 25, plot_title = NULL)

Arguments

reads_psite_list	A list of reads and their psite coordinates produced by psite_info_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.
sample	Sample to be plotted.
length_range	Range of read lengths to be included. Default: "all".
transcripts	Vector of transcript names to be included. Default: NULL (includes all transcripts).
utr5l	Length of the 5'UTR upstream of start codon to be included in the plot. Default: 25.
cdsl	Length of the cds downstream of start codon and upstream od stop codon to be included in the plot. Default: 50.
utr3l	Length of the 3'UTR downstream of stop codon to be included in the plot. Default: 25.
plot_title	Title of the plot. Default: NULL.

Details

Read metaprofiles (ribosome occupancy plots) visualize the positional distribution of reads mapping around start and stop codons.

Examples

print_rop(reads_psite_list_LMCN, annotation_human_cDNA, "<file.path>/LMCN_RPF_ribosome_occupancy_profiles_from_annotation.pdf")

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