DeconCell

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Documentation for package ‘DeconCell’ version 0.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

cell.proportions	Cell Proportion data Example cell proportions of circulating immune cell subpopulations from 5 healthy individuals
count.table	Expression data Example RNA-seq data from 5 healthy individuals
dCell.evaluate	Evaluate percentage of coeficient used in a model 'dCell.predict' Predicts cell proportions of 32 cell subpopulations usin decon Cell models.
dCell.exp.trimming	Trims a dCell.exp matrix for only dCell genes 'dCell.predict' Loads a the gene list used in all dCell models and trims a dCell.exp matrix.
dCell.expProcessing	Pre-process RNASeq based expression data. 'dCell.expProcessing' Performes a TMM normalization, log2(counts+1) and scaling.
dCell.geneList	DeconCell gene list Vector of gene names (ENSEMBL identifiers) used in all of the Decon cell models
dCell.models	DeconCell models Lists fo 33 lists containing the coefficients used in the prediction of cell proportions using expression values
dCell.names	Cell subpopulation names Code and names for the predicted cell subpopulations in the DeconCell package
dCell.predict	Predict all available cell subpopoulation in DeconCell 'dCell.predict' Runs dCell.predict
dCell.predict.single	Predict a single cell subpopoulation using a DeconCell model 'dCell.predict.single' Predicts cell proportions of one out of the 32 cell subpopulations using the DeconCell models.
dCell.run	Run Decon-cell to generate new gene signature and characterize marker genes. 'dCell.run' Runs dCell.run to generate gene expression signatures to predict cell proportions of bulk tissues
dCell.run.single	Run DeconCell to generate new gene signature for a single cell type. 'dCell.run.single' Runs dCell.run to generate gene expression signatures to predict cell proportions of bulk tissues
get.marker.genes	Wrapper function for glmnet 'get.marker.genes'
glmnet.wrapper	Wrapper function for glmnet 'glmnet.wrapper'