All functions

activate_mass_dataset()

activate_mass_dataset

add_column()

add_column

mutate_mean_intensity() mutate_median_intensity() mutate_rsd() mutate_sample_na_number() mutate_sample_na_freq() mutate_variable_na_number() mutate_variable_na_freq()

Add mean intensity for each feature to variable_info

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

check_column_name()

check_column_name

check_mass_dataset()

check_mass_dataset

check_mass_dataset_class()

check_mass_dataset_class

check_object_class()

check_object_class

convert_mass_dataset2mztab()

convert_mass_dataset2mztab

convert_mass_dataset2summarizedexperiment()

convert_mass_dataset2summarizedexperiment

convert_msdial2mass_dataset()

convert_msdial2mass_dataset

convert_mztab2mass_dataset()

convert_mztab2mass_dataset

convet_mzmine2mass_dataset()

convet_mzmine2mass_dataset

create_mass_dataset()

create_mass_dataset

export_mass_dataset()

export_mass_dataset

export_mass_dataset4metdna()

export_mass_dataset4metdna

export_ms2_data()

export_ms2_data

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() sample_info(<mass_dataset>) expression_data(<mass_dataset>) variable_info(<mass_dataset>) process_info(<mass_dataset>) ms2_data(<mass_dataset>) sample_info_note(<mass_dataset>) variable_info_note(<mass_dataset>) annotation_table(<mass_dataset>)

Extract expression_data from mass_dataset

filter_samples() filter_variables()

filter_samples

get_massdataset_version()

get_massdataset_version

ggplot_mass_dataset()

Create a ggplot object from mass_dataset class

intensity_plot()

intensity_plot

left_join_mass_dataset()

Left join for mass_dataset

mSet-class

An S4 class that stores the MS dataset from MetaboAnalystR (Prof. Jeff Xia)

mass_dataset-class

An S4 class that stores the MS dataset

massdataset_conflicts()

Conflicts between the massdataset and other packages

massdataset_logo()

massdataset_logo

massdataset_packages()

List all packages in the massdataset

merge_mass_dataset()

merge_mass_dataset

ms2_plot(<ms2_data>)

ms2_plot

write_ms2_data()

write_ms2_data

msdial_table

msdial_table feature table

mutate_ms2()

Mutate MS2 spectra for each variable

mzmine_table

zmine feature table

parse_tidymass_parameter()

parse_tidymass_parameter

cbind(<mass_dataset>) cbind_mass_dataset() rbind(<mass_dataset>) rbind_mass_dataset() head(<mass_dataset>) tail(<mass_dataset>)

cbind

read_mztab()

Read mzTab-M format data

report_parameters()

report_parameters

sample_info

Sample information

sample_info_note

Sample information note

show_missing_values()

show_missing_values

show_mz_rt_plot()

mz and rt plot

show_sample_missing_values()

show_sample_missing_values

show_variable_missing_values()

show_variable_missing_values

split_mass_dataset()

split_mass_dataset

`[`(<mass_dataset>) `$`(<mass_dataset>)

[ method

summarise_samples() summarize_samples()

merge samples

get_sample_number() get_variable_number() get_sample_id() get_variable_id() get_mv_number() dim(<mass_dataset>) nrow(<mass_dataset>) ncol(<mass_dataset>) colnames(<mass_dataset>) rownames(<mass_dataset>) apply(<mass_dataset>) intersect(<mass_dataset>,<mass_dataset>) summary(<mass_dataset>) length(<mass_dataset>) names(<mass_dataset>) dimnames(<mass_dataset>) is.na(<mass_dataset>) add_column(<mass_dataset>)

get_sample_number

tidymass_parameter-class

An S4 class that stores the parameters

translate_tidymass_parameter()

translate_tidymass_parameter

update_mass_dataset()

Update mass_dataset class object after give the one new item

update_sample_info()

update_sample_info

update_variable_info()

update_variable_info

variable_info

Variable information

variable_info_note

Variable information note