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_annotation_table(): Validate Annotation Table Format

check_column_name(): Check Whether a Column Name Is Available

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

hello_world(): Print “hello world”

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() 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>): Extraction Functions for mass_dataset Objects

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

match_mz_rt(): Match Features by m/z and Retention Time

merge_mass_dataset(): merge_mass_dataset

write_ms2_data(): write_ms2_data

ms2_plot(): Plot MS2 Spectra

msdial_table: msdial_table feature table

mutate_annotation_table(): Update Annotation Table in a mass_dataset Object

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

plot_ms2(): Plot MS2 Spectra

rbind(<mass_dataset>): rbind

rbind_mass_dataset(): Row-wise Binding of mass_dataset Objects

read_mgf(): Read MGF Files

read_mztab(): Read mzTab Data File

read_mzxml(): Read mzXML and mzML Files

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