create_tidy_omic: Create Tidy Omic

In romic: R for High-Dimensional Omic Data

Create Tidy Omic

Description

A tidy omics object contains a formatted dataset and a summary of the experimental design.

Usage

create_tidy_omic(
  df,
  feature_pk,
  feature_vars = NULL,
  sample_pk,
  sample_vars = NULL,
  omic_type_tag = "general",
  verbose = TRUE
)

Arguments

df	a data.frame (or tibble) containing some combination of feature, sample and observation-level variables
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_pk	A unique identifier for samples
sample_vars	a character vector of additional sample-level variables (or NULL if there are no additional variables)
omic_type_tag	an optional subtype of omic data: metabolomics, lipidomics, proteomics, genomics, general
verbose	extra reporting messages

Value

An S3 tidy_omic/tomic object built on a list:

data

A tibble with one row per measurement (i.e., features x samples)

design

A list which organized the dataset's meta-data:

feature_pk

variable specifying a unique feature

sample_pk

variable specifying a unique sample

features

tibble of feature attributes

samples

tibble of sample attributes

measurements

tibble of measurement attributes

Examples

library(dplyr)

measurement_df <- tidyr::expand_grid(
  feature_id = 1:10,
  sample_id = LETTERS[1:5]
) %>%
  dplyr::mutate(value = rnorm(n()))

feature_df <- tibble(
  feature_id = 1:10,
  feature_group = rep(c("a", "b"), each = 5)
)
sample_df <- tibble(
  sample_id = LETTERS[1:5],
  sample_group = c("a", "a", "b", "b", "b")
)

triple_omic <- create_triple_omic(
  measurement_df, feature_df, sample_df,
  "feature_id", "sample_id"
)
raw_tidy_omic <- triple_to_tidy(triple_omic)$data

create_tidy_omic(raw_tidy_omic,
  feature_pk = "feature_id",
  feature_vars = "feature_group", sample_pk = "sample_id",
  sample_vars = "sample_group"
)

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