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All functions

Metabolite-class Metabolite
The Metabolite class
Metabolite2maplet()
Convert a Metabolite object to maplet data
QC_pipeline()
quality control pipeline
QCmatrix_norm()
QCmatrix normalization
RSD()
RSD
anno_hmdb()
Query metabolite ID in HMDB database
assayData()
get assayData
`assayData<-`()
set assayData
batch_norm()
batch normalization
bridge()
bridge different data sets based on conversion factors
column_missing_rate()
column missing rate
correlation()
correlation of features between two Metabolite objects
create_Metabolite()
Create a Metabolite object
df_plasma
Example data.
featureData()
get featureData
`featureData<-`()
set featureData
filter_column_constant() calculate_column_constant()
filter columns if values are constant
filter_column_missing_rate()
filter columns using missing rate
filter_row_missing_rate()
filter rows using missing rate
fit_lm() fit_logistic() fit_poisson() fit_cox() fit_lme() fit_glmer() fit_lmer()
available regression methods
genuMet_makefeature()
distinguish genuine untargeted metabolic features without QC samples
impute() impute_kNN()
impute missing values
inverse_rank_transform()
rank-based inverse normal transformation
is_outlier()
is outlier
load_data()
Load metabolite data from three separate files
load_excel()
Load metabolite data from an excel file
maplet2Metabolite()
Convert maplet data to a Metabolite object
merge_data()
merge two Metabolite objects
modelling_norm()
LOESS normalization
nearestQC_norm()
nearest QC sample normalization
outlier_rate()
outlier rate
pareto_scale()
pareto scale transformation
plot_Metabolite()
plot a Metabolite object
plot_PCA()
plot PCA
plot_QC()
quality control visualization
plot_ROC()
ROC
plot_UMAP()
Plot UMAP
plot_injection_order()
injection order scatterplot
plot_tsne()
plot tSNE
plot_volcano()
volcano plot for regression results
regression() regression_each() regression_each_as_outcome()
regression analysis
replace_outlier()
change outlier values as NA or winsorize
row_missing_rate()
row missing rate
run_PCA()
Principal Components Analysis
sampleData()
get sampleData
`sampleData<-`()
set sampleData
save_data_txt()
Save metabolite data in txt files
save_data_xls()
Save metabolite data in an Excel file
show(<Metabolite>)
Print a Metabolite class object
subset()
subset a Metabolite object.
transformation()
apply transformation to a Metabolite object
update_Metabolite()
Update a Metabolite object