Curated Latent-variable Analysis with Molecular Priors

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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