Man pages for zhuchcn/Metabase
Data container, handling, and visualization for high through-put quantitative experiment data.

as_ExpressionSetConvert to an mSet object to ExpressionSet
as_phyloseqconvert a MicrobiomeSet object to phyloseq
assign_lipid_classAssign lipid class based on lipid annotation name
calibrate_lipidomics_wcmcCalculate concentration by calibrating from internal...
collapse_QCCollapse QC samples from a MetabolomcisSet object
conc_tableConstruct or assess a conc_table object
conc_table-classS4 class for concentration table
conc_table-setAssign a conc_table slot to a mSet object
data-lipid(Data) Lipidomics dataset
dim-mSet-methodGet dimemsions of the conc_table of a mSet object
experiment_dataAccess the experiment_data slot from a mSet object
ExperimentData-classDeprecated A virtual S4 class for experiment data
experiment_data-setAssign a experiment_data slot to a mSet object
export_excelExport mSet object into a excel sheet
export_txtExport mSet object to separate text files
ExtractExtract or Replace A Slot of An mSet or ExperimentData object
feature_dataConstruct or access a feature_data object
feature_data-classS4 class for feature data.
feature_data-setAssign a feature_data slot to a mSet object
featureNames-mSet-methodGet the feature names of a mSet object
filter_by_cvFilter features by QC CV
GlycomicsExperimentDataDeprecated Construction method for the S4 class...
GlycomicsExperimentData-classDeprecated S4 class to store experiment data for glycomics...
GlycomicsSetConstruct a GlycomicsSet object
GlycomicsSet-classS4 class to store glycomics experiment data
helloHello, World!
import_wcmc_excelImport West Coast Metabolomics Center data spreadsheet to a...
lipid_name_formaterLipid annotation formater for lipidblast
LipidomcisSet-classS4 class to store lipidomics dataset
LipidomicsExperimentDataConstruction method for LipidomicsExperimentData-class
LipidomicsExperimentData-classDeprecated S4 class to store experiment data for metabolomics...
LipidomicsSetConstruct a LipidomicsSet object
MetabolomicsExperimentDataDeprecated Construction method for...
MetabolomicsExperimentData-classDeprecated S4 class to store experiment data for metabolomics...
MetabolomicsSetConstruct a MetabolomicsSet object
MetabolomicsSet-classS4 class to store metabolomics experiment data
MicrobiomeExperimentDataDeprecated Construct a MicrobiomeExperimentData object
MicrobiomeExperimentData-classDeprecated S4 class to store the experiment data of a...
MicrobiomeSetMain constructor for MicrobiomeSet class
MicrobiomeSet-classS4 class to store Micorbiome Data
mSet-classA virtual S4 class to store an quantitative experiment data.
mSet_deseqRun negative bionomial bistribution based differential...
mSet_limmaRun linear model with the limma package
MultiExperimentDataS4 class to store experiment data for MultxSet
MultxSetConstruct a MultxSet class object
MultxSet-classS4 class for mutiple experiment types
mz2molwtcalculate molecular weight from m/z
nCarbonsExtract the carbon chain length from lipidome annotation
nDoubleBondsGet the number of double bonds
nFattyAcylsGet the number of fatty acyls of a given lipid annotation.
nfeatures-mSet-methodGet number of features from a mSet object
nsamples-mSet-methodGet number of samples from a mSet object
plot_boxplotMake a boxplot of a feature
plot_heatmapCreate a heatmap of an mSet object
plot_hist_NAPlot Histogram of Missing Values
plot_median_histHistogram of medians of all features after scaling.
plot_normality_boxplotPlot normality boxplot of each individual feature
plot_normality_ridgesNormality density plot of each feature
plot_pcaCreate a PCA plot
plot_qcPlot quality control from a MetabolomcisSet object
ProteomicsExperimentDataDeprecated Construction method for the S4 class...
ProteomicsExperimentData-classDeprecated S4 class to store experiment data for proteomics...
ProteomicsSetConstruct a ProteomicsSet object
ProteomicsSet-classS4 class to store proteomics experiment data
sampleNames-mSet-methodGet or set the sample names of a mSet object
sample_tableConstruction or access a sample_table object
sample_table-classS4 class for sample metadata.
sample_table-setAssign a sample_table slot to a mSet object
subset_samples-mSet-methodSubset an mSet object
summarize_ACLCalculate the average carbon chain length
summarize_EODCalculate the Equivalent Double Bond per 18 carbons
summarize_featuresSummarize mSet by a feature variable
summarize_lipid_ratiosCalculate lipid classes ratios
summarize_odd_chainCalculate odd chain lipids abundance
summarize_samplesSummarize mSet by sample variables
transform_by_featureTransform an mSet object by features
transform_by_sampleTransform an mSet object by sample
zhuchcn/Metabase documentation built on July 23, 2019, 1:36 p.m.