AUC                     Compute AUC using Wilcoxon rank-sum test
BH                      Adjust p-values using Benjamini-Hochberg method
CLAMPbase               CLAMP base matrix factorization
CLAMPdotplot            Dot plot of top pathways for a single latent
                        variable
CLAMPdotplotAll         Dot plot of pathway-LV associations across all
                        latent variables
CLAMPfull               Runs the streamlined full CLAMP model.
CLAMPfullnVP            Full CLAMP model with prior information and
                        cross-validation
CLAMPplotTopZ           Plot top genes per LV by Z loading
CLAMPplotU              Plot the U matrix (pathway-LV associations) as
                        a heatmap
allAgainstAllAUCs       Compute all-vs-all AUC matrix
binarizeTop             Binarize matrix by top-k values per column
celltypeTargets         Cell-type deconvolution matrix
cleanFBM                Clean a Filebacked Big Matrix (FBM) by
                        log-transforming and handling NAs
commonRows              Find common row names between two matrices or
                        data frames
compareBs               Compare two sets of factor loadings or
                        embeddings
computeRowStatsFBM      Compute row-wise sum and sum of squares for a
                        Filebacked Big Matrix
compute_svd             Compute a truncated SVD for a CLAMP input
                        matrix
cpmCLAMP                Compute counts-per-million (CPM) for CLAMP
                        pipelines
cpmCLAMPFBM             Compute CPM on a file-backed matrix for CLAMP
                        (in-place)
crossVal                Cross-validation AUC for CLAMP latent variables
                        and pathways
cross_ZY                Cross-product Z^T Y with FBM or dense matrices
dataWholeBlood          Whole-blood reference expression matrix
differentialLVActivity
                        Differential latent-variable activity between
                        sample groups
filterFBM               Filter rows of a Filebacked Big Matrix based on
                        mean and variance
findSplineMax           Find the location of the maximum of a smoothing
                        spline
getAUCstats             Count number of latent variables exceeding AUC
                        thresholds
getChat                 Compute Chat matrix from prior annotation
getGMT                  Download and read a GMT file from a URL
getMatchedPathwayMat    Subset and filter pathway matrix to match
                        target genes
getMatchedPathwayMat2   Subset and filter multiple pathway matrices to
                        match target genes
getMatchedPathwayMatList
                        Subset and filter multiple pathway matrices to
                        match target genes
getMatchedPathwayMatOld
                        Subset and filter pathway matrix to match
                        target genes
getMaxAUC               Get maximum AUC per latent variable
getScaleFromSVs         Estimate noise scale from singular values with
                        linear tail extrapolation
gmtListToSparseMat      Convert a list of GMT gene sets to a sparse
                        matrix
majorCellTypes          Major cell-type annotations
mat_mult                Matrix multiplication with support for FBM
                        objects
max_correspondence_greedy
                        Greedy maximum correspondence from correlation
                        matrix
mymessage               Print a concatenated message
num.pc                  Estimate number of principal components via
                        elbow or permutation method
oneToOneMask            One-to-one masking of maximum associations
panDB                   panDB gene-set database
pinv.ridge              Ridge-regularized pseudoinverse via SVD
plotTopZ_Complex        ComplexHeatmap visualization of top genes by
                        latent variable
preprocessCLAMP         Preprocess an expression matrix for CLAMP
preprocessCLAMPFBM      Preprocess a bigstatsr FBM for CLAMP
projectCLAMP            Project new data into CLAMP latent space
read_gmt                Read a GMT file into a list
ridge_B                 Ridge regression update for B
rotateSVD               Rotate SVD components to make dominant
                        directions positive
row_cor                 Row-wise correlation between two matrices
run_elbow               Run elbow method to estimate number of PCs
run_permutation         Run permutation method to estimate number of
                        PCs
select_clamp_k          Select default number of CLAMP latent variables
                        from an SVD
select_svd_k            Select default number of components for a CLAMP
                        solver SVD
solveU                  Fit the loading matrix Z using sparse
                        regression of prior information U
squashZscore            Squash extreme z-scores
tscale                  Row-wise scaling (mean 0, sd 1)
winsor_topk             Winsorize matrix columns by capping the top-k
                        values
xCell                   xCell cell-signature matrix
zscoreCLAMP             Z-score a filtered expression matrix for CLAMP
zscoreCLAMPFBM          Z-score a filtered FBM in-place
