Calculate Pairwise Sample Correlations — get_sample

Computes a pairwise correlation matrix for all samples based on their protein intensity profiles. The result is returned in a long "tidy" format data table.

Usage

get_sample_correlation(object, method = "spearman", num_features = NULL)

# S4 method for class 'SummarizedExperiment'
get_sample_correlation(object, method = "spearman", num_features = NULL)

Arguments

object: A SummarizedExperiment object.
method: The correlation method to use. Can be one of "spearman" (the default), "pearson", or "kendall".
num_features: Optional. The number of most variable proteins to use for the correlation calculation. If NULL (the default), all proteins are used.

Value

A data.table with three columns: SampleA, SampleB, and a third column named for the method used (e.g., Spearman), containing the pairwise correlation coefficients.