data_list: Build a 'data_list' class object

In metasnf: Meta Clustering with Similarity Network Fusion

Build a data_list class object

Description

data_list() constructs a data list object which inherits from classes data_list and list. This object is the primary way in which features to be used along the metasnf clustering pipeline are stored. The data list is fundamentally a 2-level nested list object where each inner list contains a data frame and associated metadata for that data frame. The metadata includes the name of the data frame, the 'domain' of that data frame (the broader source of information that the input data frame is capturing, determined by user's domain knowledge), and the type of feature stored in the data frame (continuous, discrete, ordinal, categorical, or mixed).

Usage

data_list(..., uid)

Arguments

...	Any number of lists formatted as (df, "df_name", "df_domain", "df_type") and/or any number of lists of lists formatted as (df, "df_name", "df_domain", "df_type").
uid	(character) the name of the uid column currently used data. data frame.

Examples

heart_rate_df <- data.frame(
    patient_id = c("1", "2", "3"),
    var1 = c(0.04, 0.1, 0.3),
    var2 = c(30, 2, 0.3)
)

personality_test_df <- data.frame(
    patient_id = c("1", "2", "3"),
    var3 = c(900, 1990, 373),
    var4 = c(509, 2209, 83)
)

survey_response_df <- data.frame(
    patient_id = c("1", "2", "3"),
    var5 = c(1, 3, 3),
    var6 = c(2, 3, 3)
)

city_df <- data.frame(
    patient_id = c("1", "2", "3"),
    var7 = c("toronto", "montreal", "vancouver")
)

# Explicitly (Name each nested list element):
dl <- data_list(
    list(
        data = heart_rate_df,
        name = "heart_rate",
        domain = "clinical",
        type = "continuous"
    ),
    list(
        data = personality_test_df,
        name = "personality_test",
        domain = "surveys",
        type = "continuous"
    ),
    list(
        data = survey_response_df,
        name = "survey_response",
        domain = "surveys",
        type = "ordinal"
    ),
    list(
        data = city_df,
        name = "city",
        domain = "location",
        type = "categorical"
    ),
    uid = "patient_id"
)

# Compact loading
dl <- data_list(
    list(heart_rate_df, "heart_rate", "clinical", "continuous"),
    list(personality_test_df, "personality_test", "surveys", "continuous"),
    list(survey_response_df, "survey_response", "surveys", "ordinal"),
    list(city_df, "city", "location", "categorical"),
    uid = "patient_id"
)

# Printing data list summaries
summary(dl)

# Alternative loading: providing a single list of lists
list_of_lists <- list(
    list(heart_rate_df, "data1", "domain1", "continuous"),
    list(personality_test_df, "data2", "domain2", "continuous")
)

dl <- data_list(
    list_of_lists,
    uid = "patient_id"
)

metasnf documentation built on April 3, 2025, 5:40 p.m.