GetSimilarFeatures: GetSimilarFeatures

In atlasapprox: Cell Atlas Approximations

GetSimilarFeatures

Description

Get features with similar expression patterns to a specified feature in a given organism and organ.

Usage

GetSimilarFeatures(organism, organ, feature, number, method)

Arguments

organism	The organism you would like to query
organ	The organ you would like to query
feature	The feature to find similarities for
number	The number of similar features you would like to get.
method	The method used to compute similarity between features. The following methods are available: - correlation (default): Pearson correlation of the fraction_detected - cosine: Cosine similarity/distance of the fraction_detected - euclidean: Euclidean distance of average measurement (e.g. expression) - manhattan: Taxicab/Manhattan/L1 distance of average measurement - log-euclidean: Log the average measurement with a pseudocount of 0.001, then compute euclidean distance. This tends to highlight sparsely measured features

Value

A dataframe of similar features and their distances from the focal feature according to the method chosen

Examples

GetSimilarFeatures("h_sapiens", "lung", "PTPRC", 5, "correlation")

atlasapprox documentation built on Oct. 25, 2024, 9:07 a.m.