Package index • MetaboCrates

All functions

-package MetaboCrates: MetaboCrates

add_group(): Group data

calculate_CV(): Calculate CV for different QC samples for each metabolite

check_values(): Convert weird values into NA's

complete_data(): Complete not quantified values

create_PCA_plot(): PCA plot

create_beeswarm_plot(): Beeswarm Plot of Metabolite Values

create_boxplot(): Boxplots of individual metabolite values before and after imputation

create_correlations_heatmap(): Heatmap of correlations between metabolites

create_distribution_plot(): Histograms, density or beeswarm plots of individual metabolite values before and after imputation

create_plot_of_2_metabolites(): Plot of two metabolites

create_qqplot(): QQ plots of individual metabolite values before and after imputation

create_venn_diagram(): Venn diagram for group levels

get_CV_to_remove(): Get CV to remove

get_LOD_to_remove(): Get metabolites to remove based on missing values proportion

get_example_data(): Get path to example data

get_info(): Get information about data

pca_variance(): Plot of variance explained by principal components

plot_NA_percent(): Barplot of missing values proportion in each metabolite

plot_groups(): Barplot of group level sizes

plot_heatmap(): Heatmap of missing values

plot_mv_types(): Barplot of missing values types

raw_data(): raw_data class

read_data(): Read Biocrates data

remove_metabolites(): Add metabolites to the attribute removed

show_data(): Show metabolites without removed ones

show_ratios(): Show missing values ratios without those in the removed metabolites

unremove_all(): Setting the specified type in attribute removed to NULL

unremove_metabolites(): Removing the specified metabolites from the attribute removed