buildReference          Function for building a Symphony reference
                        starting from expression matrix
buildReferenceFromHarmonyObj
                        Function for building a Symphony reference from
                        a Harmony object. Useful if you would like your
                        code to be more modular. Note that you must
                        have saved vargenes_means_sds and PCA loadings.
calcPerCellMappingMetric
                        Per-cell Confidence Score: Calculates the
                        weighted Mahalanobis distance for the query
                        cells to reference clusters. Returns a vector
                        of distance scores, one per query cell. Higher
                        distance metric indicates less confidence.
calcPerClusterMappingMetric
                        Per-cluster Confidence Score: Calculates the
                        Mahalanobis distance from user-defined query
                        clusters to their nearest reference centroid
                        after initial projection into reference PCA
                        space. All query cells in a cluster get the
                        same score. Higher distance indicates less
                        confidence. Due to the instability of
                        estimating covariance with small numbers of
                        cells, we do not assign a score to clusters
                        smaller than u * d, where d is the
                        dimensionality of the embedding and u is
                        specified.
calcknncorr             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).
calcknncorrWithinQuery
                        Calculates the k-NN correlation within the
                        query cells only, which measures how well the
                        sorted ordering of k nearest query neighbors in
                        a query de novo PCA embedding correlate with
                        the ordering for the cells in the reference
                        mapping embedding.
evaluate                Function for evaluating F1 by cell type,
                        adapted from automated cell type identifiaction
                        benchmarking paper (Abdelaal et al. Genome
                        Biology, 2019)
findVariableGenes       Function to find variable genes using mean
                        variance relationship method
knnPredict              Predict annotations of query cells from the
                        reference using k-NN method
mapQuery                Function for mapping query cells to a Symphony
                        reference
pbmcs_exprs_small       Log(CP10k+1) normalized counts matrix (genes by
                        cells) for 10x PBMCs dataset for vignette.
pbmcs_meta_small        Metadata for 10x PBMCs dataset for vignette.
plotReference           Function to plot reference, colored by cell
                        type
rowSDs                  Calculate standard deviations by row
runPCAQueryAlone        Runs a standard PCA pipeline on query (1
                        batch). Assumes query_exp is already
                        normalized.
scaleDataWithStats      Scale data with given mean and standard
                        deviations
symphony                symphony
vargenes_vst            Function to find variable genes using variance
                        stabilizing transform (vst) method
