run_ca: run_ca

In ahnjedid/MetaConIdentifier: Metadata Confounding Identifier

Description

The core function which runs the correspondence analysis (CA) on the metadata. Two preprocessing steps are performed beforehand:

1. Transformation of the metadata so that different variable types could be recoded into one common format without loss or sacrifice of information and into a variable type compatible with CA. They will be performed using the ours R package.

2. Imputation of the metadata to handle any missing values. It will be performed using the missMDA R package.

Usage

run_ca(metadata)

Arguments

metadata

The cleaned metadata after running standardize_metadata().

Value

A list containing 3 objects.

• ca_obj - The CA object returned from the ExPosition function. This object will be used to plot the components through plot_components().

• fi_var - A vector representing the percentage of explained variance for each factor. The elbow method can be used through identify_elbow().

• fi_mat - A matrix of factor scores for the observations/rows. This matrix can be visualized through plot_factor_scores().

Examples

# Using tcga_metadata from package.
library(MetaConIdentifier)
ca_info <- run_ca(tcga_meta_clean)

# Obtain full matrix of factor scores for the observations/rows.
ca_info$fi_mat

ahnjedid/MetaConIdentifier documentation built on Dec. 18, 2021, 11:26 p.m.