Man pages for wgmao/PLIER
Pathway-Level Information Extractor (PLIER): a generative model for gene expression data

bloodCellMarkersIRISDMAPBlood cell markers
canonicalPathwaysCanonical Pathways
chemgenPathwaysChemgen Pathways
combinePathscombines binary pathway matricies into one, rownames are...
commonRowsreturns the row names in common
computeChatComputes the ridge pseudo-inverse of the prior information...
CTNNB1mutImmune Markers (Clinical Pathways)
DataSmoothSVD based smoothing for single cell RNAseq data
getCutoffget the p-value cutoff for a specific FDR
HCCDataHepatocellular carcinoma (HCC) Data
immunePathwaysImmune Pathways
mapPathwayRename pathway matrix gene names. Useful for species...
nameBnames latent variables according to their pathway useage (if...
num.pcestimates the number of 'significant' principle components...
oncogenicPathwaysOncogenic Pathways
PLIERMain PLIER function
plierResToMarkersCreates a binary cell-type marker matrix using prior results....
plotMatgeneric function to plot the non-zero elements of a sparse...
plotTopZvisualize the top genes contributing to the LVs
plotTopZallPathvisualize the top genes contributing to the LVs similarily to...
plotUplot the U matrix from a PLIER decomposition
rowNormz-score each row of the data
SPVsSurrogate Proportion Variables
svmMarkersBlood cell markers
vacDataVaccination Data
wgmao/PLIER documentation built on Oct. 10, 2018, 10:25 p.m.