# Curated Latent-variable Analysis with Molecular Priors

## Documentation for package ‘CLAMP’ version 0.99.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

allAgainstAllAUCs | Compute all-vs-all AUC matrix
AUC | Compute AUC using Wilcoxon rank-sum test
BH | Adjust p-values using Benjamini-Hochberg method
binarizeTop | Binarize matrix by top-k values per column
celltypeTargets | Cell-type deconvolution matrix
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
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