calcknncorr {symphony} | R Documentation |
Calculates the k-NN correlation, which measures how well the sorted ordering of k nearest reference neighbors in a gold standard embedding correlate with the ordering for the same reference cells in an alternative embedding (i.e. from reference mapping). NOTE: it is very important for the order of reference cells (cols) in gold_ref matches that of alt_ref (same for matching columns of gold_query and alt_query).
Description
Calculates the k-NN correlation, which measures how well the sorted ordering of k nearest reference neighbors in a gold standard embedding correlate with the ordering for the same reference cells in an alternative embedding (i.e. from reference mapping). NOTE: it is very important for the order of reference cells (cols) in gold_ref matches that of alt_ref (same for matching columns of gold_query and alt_query).
Usage
calcknncorr(gold_ref, alt_ref, gold_query, alt_query, k = 500)
Arguments
gold_ref |
Reference cells in gold standard embedding (PCs by cells) |
alt_ref |
Reference cells in alternative embedding (PCs by cells) |
gold_query |
Query cells in gold standard embedding (PCs by cells) |
alt_query |
Query cells in alternative embedding (PCs by cells) |
k |
Number of reference neighbors to use for kNN-correlation calculation |
Value
Vector of k-NN correlations for query cells
[Package symphony version 0.1.1 Index]