romic (version 1.1.3)

convert_wide_to_tidy_omic: Convert Wide to Tidy Omic

Description

Convert a wide dataset of species' abundances (gene product, metabolites, lipids, ...) into a triple_omic dataset (one observation per row)

Usage

convert_wide_to_tidy_omic(
  wide_df,
  feature_pk,
  feature_vars = NULL,
  sample_var = "sample",
  measurement_var = "abundance",
  omic_type_tag = "general",
  verbose = TRUE
)

Value

A tidy_omic object as produced by create_tidy_omic.

Arguments

wide_df

a data.frame (or tibble) containing 1+ columns of feature attributes and many columns of samples

feature_pk

A unique identifier for features

feature_vars

a character vector of additional feature-level variables (or NULL if there are no additional variables)

sample_var

variable name to use for samples

measurement_var

variable name to use for measurements

omic_type_tag

an optional subtype of omic data: metabolomics, lipidomics, proteomics, genomics, general

verbose

extra reporting messages

Examples

library(dplyr)

wide_measurements <- brauer_2008_triple[["measurements"]] %>%
  tidyr::spread(sample, expression)

wide_df <- brauer_2008_triple[["features"]] %>%
  left_join(wide_measurements, by = "name")

convert_wide_to_tidy_omic(wide_df,
  feature_pk = "name",
  feature_vars = c("BP", "MF", "systematic_name")
)