Package index
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rRMSAnalyzer
rRMSAnalyzer-package
- rRMSAnalyzer package dedicated to analysis of RiboMethSeq data
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ribo_toy
- RiboClass from a toy dataset
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human_methylated
- Known 2'Ome positions in Human rRNA
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human_suspected
- Suspected 2'Ome positions in Human rRNA
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human_both_methylated_and_suspected
- Known and suspected 2'Ome positions in Human rRNA
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annotate_site()
- Annotate sites according to a dataframe containing annotation
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get_annotation()
- Get annotation of a RiboClass
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remove_annotation()
- Remove site annotations of a given RiboClass
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keep_selected_annotation()
- Keep only a subset of the current annotation
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load_ribodata()
- Load csv files from GenomeCov and their associated metadata. Create a RiboClass.
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new_riboclass()
- Create a RiboClass from count files and metadata.
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compute_cscore()
- Compute c-score for all samples in a riboclass
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adjust_bias()
- Correct batch effect with ComBat-seq method
RiboClass customization
Customize an already generated RiboClass, by renaming/removing RNA or remove a sample.
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show_rna_names()
- Display RNA names
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rename_rna()
- Rename RNAs in a RiboClass object
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remove_rna()
- Remove one or more RNA among your RiboClass' samples
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remove_ribo_samples()
- Remove samples from a Riboclass object
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keep_ribo_samples()
- Keep only selected samples from a RiboClass Object.
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get_2ome_summary()
- Create a metric summary table for 2ome_analysis report
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get_diff_sites_summary()
- Get a summary of statistics for differential 2'ome-sites analysis
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get_IQR()
- Compute IQR or variance for 2'Ome sites
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get_outliers()
- Create a outlier summary table (used in plot_heatmap_annotated)
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get_variant_sites()
- Return the most/less variant sites of a dataframe or a RiboClass
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render_html_welch()
- Print Welch result in report
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render_html_wilcoxon()
- Print Wilcoxon result in report
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compute_pval()
- Compute statistics (p-value for, Welch, Wilcoxon, Kruskal, ANOVA test) for C-score based on condition column
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plot_coa()
- Correspondence analysis of a RiboClass' counts
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plot_comparison_median()
- Plot comparison of median of C-score between two conditions
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plot_counts_env()
- Plot counts for a given position on a given RNA
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plot_counts_fraction()
- Plot count distribution among RNAs for each sample
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plot_diff_sites()
- Plot sites showing statistical difference between conditions
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plot_global_profile()
- Plot global profile for given conditions on a given metadata
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plot_heatmap()
- Plot heatmap for a riboclass object
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plot_heatmap_annotated()
- Plot a correlation heatmap from a RiboClass object
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plot_heatmap_corr()
- Plot a correlation heatmap from a riboclass object Shows the correlation distance between samples.
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plot_pca()
- Principal component analysis of a RiboClass object
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plot_rlc()
- Relative Log Expression plot of a RiboClass object’s counts
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plot_sites_by_IQR()
- Plot sites in increasing/decreasing order of IQR or variance
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plot_stat()
- Plot statistic of significant differential sites between experimental condition returned by the res.pv function
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boxplot_count()
- Plot a boxplot of a RiboClass object counts
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boxplot_cscores()
- Plot boxplot representing the C-score values of all samples for each individual annotated site Sites are sorted by their median.
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extract_data()
- Aggregate results into a single matrix
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format_to_plot()
- Transform RiboClass data to a "ggplot-friendly" data frame.
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mean_samples_by_condition()
- Regroup samples by condition and calculate mean for each condition
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report_qc()
- Generate html report about possible batch effect for a given RiboClass.