convert_wide_to_tidy_omic: Convert Wide to Tidy Omic

In romic: R for High-Dimensional Omic Data

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
)

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

Value

A tidy_omic object as produced by create_tidy_omic.

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")
)

romic documentation built on Sept. 21, 2023, 9:06 a.m.