Package index • massdataset

All functions
`activate_mass_dataset()`	Activate a Specific Dataset
`adjust_confounder()`	Adjust Confounders in a mass_dataset Object
`apply(<mass_dataset>)`	apply
`log(<mass_dataset>)` `abs(<mass_dataset>)` `sqrt(<mass_dataset>)` `scale(<mass_dataset>)` `+`(<mass_dataset>,<numeric>) `-`(<mass_dataset>,<numeric>) `*`(<mass_dataset>,<numeric>) `/`(<mass_dataset>,<numeric>) `>`(<mass_dataset>,<numeric>) `>=`(<mass_dataset>,<numeric>) `<`(<mass_dataset>,<numeric>) `<=`(<mass_dataset>,<numeric>) `==`(<mass_dataset>,<numeric>) `colSums(<mass_dataset>)` `rowSums(<mass_dataset>)` `colMeans(<mass_dataset>)` `rowMeans(<mass_dataset>)`	Log-transform Expression Data in `mass_dataset` Object
`$`(<mass_dataset>)	$ method
`cbind(<mass_dataset>)`	cbind
`cbind_mass_dataset()`	cbind mass_data class
`check_column_name()`	check_column_name
`check_mass_dataset()`	Check Mass Dataset
`check_mass_dataset_class()`	Check the Validity of a mass_dataset Object
`check_object_class()`	Check Object Class
`colnames(<mass_dataset>)`	colnames
`convert_mass_dataset2mztab()`	Convert mass_dataset to mzTab Format
`convert_mass_dataset2summarizedexperiment()`	Convert mass_dataset to SummarizedExperiment Object
`convert_msdial2mass_dataset()`	Convert MS-Dial Data to mass_dataset Object
`convert_mztab2mass_dataset()`	Convert mzTab Data to mass_dataset Object
`convet_mzmine2mass_dataset()`	Convert MZmine Data to mass_dataset Object
`create_mass_dataset()`	Create a New mass_dataset Object
`dim(<mass_dataset>)`	dim
`dimnames(<mass_dataset>)`	dimnames
`export_mass_dataset()`	Export mass_dataset Object to Files
`export_mass_dataset4metdna()`	Export mass_dataset Object for MetDNA Analysis
`export_ms2_data()`	Export MS2 Data from mass_dataset Object
`expression_data`	Expression data
`filter_samples()` `filter_variables()`	filter_samples
`get_massdataset_version()`	Retrieve the Version of MassDataset Package
`ggplot_mass_dataset()`	Create ggplot2 Visualization for a mass_dataset Object
`head(<mass_dataset>)`	head
`intensity_plot()`	Create Intensity Plot for a Variable in a mass_dataset Object
`intersect(<mass_dataset>,<mass_dataset>)`	intersect
`is.na(<mass_dataset>)`	is.na
`left_join_mass_dataset()`	Left join for mass_dataset
`length(<mass_dataset>)`	length
`mSet-class`	An S4 class that stores the MS dataset from MetaboAnalystR (Prof. Jeff Xia)
`mass_dataset-class`	S4 Class Representing a mass_dataset
`extract_expression_data()` `extract_sample_info()` `extract_variable_info()` `extract_annotation_table()` `extract_variable_info_note()` `extract_sample_info_note()` `extract_process_info()` `extract_ms2_data()`	Extract Components from mass_dataset Object
`get_sample_number()` `get_variable_number()` `get_sample_id()` `get_variable_id()` `get_mv_number()`	Get Some Information of a mass_dataset Object
`massdataset_conflicts()`	Conflicts between the massdataset and other packages
`massdataset_logo()`	Display the MassDataset Logo
`massdataset_packages()`	List all packages in the massdataset
`merge_mass_dataset()`	merge_mass_dataset
`write_ms2_data()`	write_ms2_data
`msdial_table`	msdial_table feature table
`mutate_mean_intensity()`	Add Mean Intensity to mass_dataset Object
`mutate_median_intensity()`	Add Median Intensity to mass_dataset Object
`mutate_ms2()`	Mutate MS2 Data in mass_dataset Object
`mutate_rsd()`	Mutate Relative Standard Deviation (RSD) in mass_dataset Object
`mutate_sample_na_freq()`	Mutate Sample NA Frequency in mass_dataset Object
`mutate_sample_na_number()`	Mutate Sample NA Count in mass_dataset Object
`mutate_sample_zero_freq()`	Mutate Sample Zero Frequency in mass_dataset Object
`mutate_sample_zero_number()`	Mutate Sample Zero Number in mass_dataset Object
`mutate_variable_na_freq()`	Mutate Variable NA Frequency in mass_dataset Object
`mutate_variable_na_number()`	Mutate Variable NA Count in mass_dataset Object
`mutate_variable_zero_freq()`	Mutate Variable Zero Frequency in mass_dataset Object
`mutate_variable_zero_number()`	Mutate Variable Zero Number in mass_dataset Object
`mzmine_table`	zmine feature table
`names(<mass_dataset>)`	names
`ncol(<mass_dataset>)`	ncol
`nrow(<mass_dataset>)`	nrow
`parse_tidymass_parameter()`	Parse tidymass_parameter Object to Data Frame
`rbind(<mass_dataset>)`	rbind
`rbind_mass_dataset()`	Row-wise Binding of mass_dataset Objects
`read_mztab()`	Read mzTab Data File
`report_parameters()`	Generate Parameter Report for mass_dataset Object
`rownames(<mass_dataset>)`	rownames
`sample_info`	Sample information
`sample_info_note`	Sample information note
`show_missing_values()`	show_missing_values
`show_mz_rt_plot()`	Generate mz-rt Plot for mass_dataset Object
`show_sample_missing_values()`	show_sample_missing_values
`show_variable_missing_values()`	show_variable_missing_values
`split_mass_dataset()`	Split and Update mass_dataset Object Based on Criteria
`[`(<mass_dataset>)	[ method
`summarise_samples()` `summarize_samples()`	merge samples
`summary(<mass_dataset>)`	summary
`tail(<mass_dataset>)`	tail
`tidymass_parameter-class`	tidymass_parameter S4 Class
`translate_tidymass_parameter()`	Translate tidymass_parameter Object to Data Frame
`update_mass_dataset()`	Update a mass_dataset Object
`update_sample_info()`	Update Sample Information in a mass_dataset Object
`update_variable_info()`	Update Variable Information in a mass_dataset Object
`variable_info`	Variable information
`variable_info_note`	Variable information note

Reference

All functions