phData: Generic function to access the phenotypic data (Biobase)

In sipss/NIHSlcms: Signal processing of LC-MS metabolomics

Description

It uses Biobase::pData to access phenotypic data such as metadata, covariates, etc...

Usage

phData(object)

Arguments

object

Object, possibly derived from eSet-class or AnnotatedDataFrame.

Value

phenoData returns an object containing information on both variable values and variable meta-data. varLabels returns a character vector of measured variables. pData returns a data frame with samples as rows, variables as columns. varMetadata returns a data frame with variable names as rows, description tags (e.g., unit of measurement) as columns.

See Also

Other metadata functions: lcms_meta_add(), lcms_meta_export(), lcms_meta_read()

Other dataset functions: IPO_group_peaks(), find_peaks_cwp(), lcms_dataset_load(), lcms_dataset_save(), lcms_fill_chrom_peaks(), lcms_filter_mz(), lcms_filter_polarity(), lcms_filter_rt_min(), lcms_filter_sample_type(), lcms_meta_add(), lcms_meta_export(), lcms_plot_chrom_peak_image(), lcms_plot_tics(), lcms_rearrange_datafiles_by_class(), lcms_retention_time_alignment_plot(), lcms_tics(), obiAdjust_Rtime(), peakpicking_optimization()

Other import/export functions: lcms_convert_ipo_to_xcms(), lcms_dataset_load(), lcms_dataset_save(), lcms_identify_metabolites(), lcms_meta_export(), lcms_meta_read(), lcms_peak_annotation(), lcms_raw_data(), lcms_read_ipo_to_xcms(), lcms_read_samples(), lcms_rearrange_datafiles_by_class(), lcms_sig_peaks_table(), lcms_spectral_sig_features(), lcms_to_mait(), lcms_write_opt_params(), lcms_write_parameter_table()

Examples

## Not run: 
dataset <- lcms_dataset_load(system.file("extdata",
                                         "dataset.rds",
                                          package = "AlpsLCMS"))
xlsx_file <- system.file("extdata", "exported_metadata.xlsx", package = "AlpsLCMS")
metadata<- readxl::read_excel(xlsx_file)
dataset_metadata <- lcms_meta_add(dataset, metadata, by = "sampleNames")

head(phData(dataset_metadata))[1:4]

## End(Not run)

sipss/NIHSlcms documentation built on May 13, 2021, 6:19 p.m.