get_metagene_data: Get 5'/P-site profile data for metagene analysis

In ohlerlab/RiboseQC: RiboseQC, a Comprehensive Ribo-Seq Analysis Tool

Get 5'/P-site profile data for metagene analysis

Description

This function processes profile data generated by RiboseQC_analysis.

This data is used as input in plot_metagene_hm to generate plot for the Ribo-seQC report in section 4.1/4.3.

Usage

get_metagene_data(data, profile_type, res, comp)

Arguments

res	Resolution (subcodon or bins) Subcodon resolution: five_prime_subcodon (in order to call res_all$profiles_fivepr$five_prime_subcodon) or P_sites_subcodon (in order to call res_all$profiles_P_sites$P_sites_subcodon) Read coverage for the first 25nt after the transcription start site (TSS), 25nt before and 33nt after the start codon, 33nt from the middle of the CDS, 33nt before and 25nt after the stop codon, and the last 25nt before the transcription end site (TES). Bins: five_prime_bins (in order to call res_all$profiles_fivepr$five_prime_bins) or P_sites_bins (in order to call res_all$profiles_P_sites$P_sites_bins) Read coverage for 50 bins between TSS and start codon, 100 bins for the CDS, and 50 after stop codon to TES.
comp	String for originating compartment Check for available originating compartments in the data set using: names(res_all$profiles_fivepr$five_prime_subcodon)
profiles	5' or P-site profile data generated by RiboseQC_analysis: res_all$profiles_fivepr or res_all$profiles_P_sites Consists of DataFrames each containing counts of 5' or P-site profiles, calculated for different resolution types (see parameter res), originating compartments (see parameter comp), and read lengths per input sample. Example to access DataFrame: res_all$profiles_fivepr[[res]][[comp]][[read_length]] or res_all$profiles_P_sites[[res]][[comp]][[read_length]]

Value

This function returns data profile_data as list(data_single, data_all, res) with profile data

• for all read lengths individually (profile_data[1]] is data_single) and

• for all read lenghts summarized (profile_data[[2]] is data_all).

with different scaling: no scaling (none), log2 scaling (log2), and z scoring (zscore), accessable via e.g. profile_data[[1]]$none or profile_data[[2]]$zscore.

profile_data[[3]] saves the resolution type res for later use during plotting.

profile_data[[4]] stores information on whether data represents 5' or P site profiles (profile_type) for later use during plotting.

Author(s)

Dominique Sydow, [e-mail]

See Also

create_html_report

ohlerlab/RiboseQC documentation built on Aug. 15, 2023, 7:30 a.m.