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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 rRNA
human_suspected
Suspected 2'Ome positions in Human rRNA
human_both_methylated_and_suspected
Known and suspected 2'Ome positions in Human rRNA

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

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

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