Package index • rRMSAnalyzer

rRMSAnalyzer

rRMSAnalyzer rRMSAnalyzer-package: rRMSAnalyzer package dedicated to analysis of RiboMethSeq data

Example data

Example data shipped with rRMSAnalyzer.

ribo_toy: RiboClass from a toy dataset

Annotation data

Annotation data shipped with rRMSAnalyzer.

human_methylated: Known 2'Ome positions in human rRNAs

human_suspected: Suspected 2'Ome positions in human rRNAs

human_both_methylated_and_suspected: Known and suspected 2'Ome positions in human rRNAs

RiboClass annotation

Functions to add, remove or keep selected annotation in a RiboClass.

annotate_site(): Annotate sites according to a dataframe containing annotation

get_annotation(): Get annotation of a RiboClass

remove_annotation(): Remove site annotations of a given RiboClass

keep_selected_annotation(): Keep only a subset of the current annotation

Data importation

Import data to rRMSAnalyzer and generate a RiboClass.

load_ribodata(): Load csv files from GenomeCov and their associated metadata. Create a RiboClass.

new_riboclass(): Create a RiboClass from count files and metadata.

C-score computation and adjustment

Annotation data shipped with rRMSAnalyzer.

compute_cscore(): Compute c-score for all samples in a riboclass

adjust_bias(): Correct batch effect with ComBat-seq method

RiboClass customization

Customize an already generated RiboClass, by renaming/removing RNA or remove a sample.

show_rna_names(): Display RNA names

rename_rna(): Rename RNAs in a RiboClass object

remove_rna(): Remove one or more RNA among your RiboClass' samples

remove_ribo_samples(): Remove samples from a Riboclass object

keep_ribo_samples(): Keep only selected samples from a RiboClass Object.

Utils

compute_pval(): Compute statistics (p-value for, Welch, Wilcoxon, Kruskal, ANOVA test) for C-score based on condition column

get_2ome_summary(): Create a metric summary table for 2ome_analysis report

get_diff_sites_summary(): Get a summary of statistics for differential 2'ome-sites analysis

get_IQR(): Compute IQR or variance for 2'Ome sites and return a dataframe

get_outliers(): Create a outlier summary table (used in plot_heatmap_annotated)

get_variant_sites(): Return the most/less variant sites of a dataframe or a RiboClass

render_html_welch(): Print Welch result in report

render_html_wilcoxon(): Print Wilcoxon result in report

Plots

Different plots to show either samples and sites.

plot_coa(): Correspondence analysis of a RiboClass' counts

plot_comparison_median(): Plot comparison of median of C-score between two conditions

plot_counts_env(): Plot counts for a given position on a given RNA

plot_counts_fraction(): Plot count distribution among RNAs for each sample

plot_diff_sites(): Plot sites showing statistical difference between conditions

plot_global_profile(): Plot global profile for given conditions on a given metadata

plot_heatmap(): Plot heatmap for a riboclass object

plot_heatmap_annotated(): Plot a correlation heatmap from a RiboClass object

plot_heatmap_corr(): Plot a correlation heatmap from a riboclass object Shows the correlation distance between samples.

plot_pca(): Principal component analysis of a RiboClass object

plot_rlc(): Relative Log Expression plot of a RiboClass object’s counts

plot_sites_by_IQR(): Plot sites in increasing/decreasing order of IQR or variance

plot_stat(): Plot statistic of significant differential sites between experimental condition returned by the res.pv function

boxplot_count(): Plot a boxplot of a RiboClass object counts

boxplot_cscores(): Plot boxplot representing the C-score values of all samples for each individual annotated site Sites are sorted by their median.

Export data

Export data

extract_data(): Aggregate results into a single matrix

format_to_plot(): Transform RiboClass data to a "ggplot-friendly" data frame.

mean_samples_by_condition(): Regroup samples by condition and calculate mean for each condition

Reports

Generate automated reports from a RiboClass

report_2ome_sites(): Generate html report about the analysis of 2’Ome profile

report_diff_sites(): Generate html report about the statistical analysis of difference in 2’Ome level at each site

report_qc(): Generate html report about possible batch effect for a given RiboClass.