assayData | get assayData |
assayData-method | get assayData |
assayData<- | set assayData |
assayData<--method | set assayData |
batch_norm | batch normalization |
bridge | bridge different data sets based on conversion factors |
column_missing_rate | column missing rate |
column_missing_rate.default | column missing rate |
column_missing_rate.Metabolite | 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-method | get featureData |
featureData<- | set featureData |
featureData<--method | set featureData |
filter_column_constant | filter columns if values are constant |
filter_column_constant.default | filter columns if values are constant |
filter_column_constant.Metabolite | filter columns if values are constant |
filter_column_missing_rate | filter columns using missing rate |
filter_column_missing_rate.default | filter columns using missing rate |
filter_column_missing_rate.Metabolite | filter columns using missing rate |
filter_row_missing_rate | filter rows using missing rate |
filter_row_missing_rate.default | filter rows using missing rate |
filter_row_missing_rate.Metabolite | filter rows using missing rate |
fit_cox | available regression methods |
fit_glmer | available regression methods |
fit_lm | available regression methods |
fit_lme | available regression methods |
fit_lmer | available regression methods |
fit_logistic | available regression methods |
fit_poisson | available regression methods |
impute | impute missing values |
impute.default | impute missing values |
impute.Metabolite | impute missing values |
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 |
merge_data | merge two Metabolite objects |
Metabolite | The Metabolite class |
Metabolite-class | The Metabolite class |
modelling_norm | LOESS normalization |
nearestQC_norm | nearest QC sample normalization |
outlier_rate | outlier rate |
outlier_rate.data.frame | outlier rate |
outlier_rate.default | outlier rate |
outlier_rate.Metabolite | outlier rate |
pareto_scale | pareto scale transformation |
plot_injection_order | injection order scatterplot |
plot_Metabolite | plot a Metabolite object |
plot_PCA | plot PCA |
plot_ROC | ROC |
plot_tsne | plot tSNE |
plot_UMAP | Plot UMAP |
plot_volcano | volcano plot for regression results |
QCmatrix_norm | QCmatrix normalization |
QC_pipeline | quality control pipeline |
regression | regression analysis |
regression_each | regression analysis |
replace_outlier | change outlier values as NA or winsorize |
replace_outlier.data.frame | change outlier values as NA or winsorize |
replace_outlier.default | change outlier values as NA or winsorize |
replace_outlier.Metabolite | change outlier values as NA or winsorize |
row_missing_rate | row missing rate |
row_missing_rate.default | row missing rate |
row_missing_rate.Metabolite | row missing rate |
RSD | RSD |
run_PCA | Principal Components Analysis |
sampleData | get sampleData |
sampleData-method | get sampleData |
sampleData<- | set sampleData |
sampleData<--method | set sampleData |
save_data | Save metabolite data |
show-method | Print a Metabolite class object |
subset | subset a Metabolite object. |
subset.Metabolite | subset a Metabolite object. |
transformation | apply transformation to a Metabolite object |
update_Metabolite | Update a Metabolite object |