Dimensionality reduction of (single-cell) omics data in R using omicsGMF

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Documentation for package ‘omicsGMF’ version 1.0.0

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

Help Pages

calculateCVGMF	Perform a stochastic gradient descent generalized matrix factorization (sgdGMF) on cells, based on the expression or mass spectrometry data in a SingleCellExperiment, SummarizedExperiment or QFeatures object.
calculateCVGMF-method	Perform a stochastic gradient descent generalized matrix factorization (sgdGMF) on cells, based on the expression or mass spectrometry data in a SingleCellExperiment, SummarizedExperiment or QFeatures object.
calculateGMF	Perform a stochastic gradient descent generalized matrix factorization (sgdGMF) on cells or bulk samples, based on the expression or mass spectrometry data in a SingleCellExperiment, SummarizedExperiment or QFeatures object.
calculateGMF-method	Perform a stochastic gradient descent generalized matrix factorization (sgdGMF) on cells or bulk samples, based on the expression or mass spectrometry data in a SingleCellExperiment, SummarizedExperiment or QFeatures object.
calculateRankGMF	Perform an eigendecomposition for model selection based on a screeplot.
calculateRankGMF-method	Perform an eigendecomposition for model selection based on a screeplot.
imputeGMF	Impute missing values based on the results of runGMF.
imputeGMF-method	Impute missing values based on the results of runGMF.
plotCV	Functions to create a scree plot for model selection.
plotGMF	Wrapper functions to create plots for specific types of reduced dimension results in a SingleCellExperiment object, similar as the 'scater' package.
plotRank	Functions to create a scree plot for model selection.
plot_cv	Functions to create a scree plot for model selection.
plot_cv-method	Functions to create a scree plot for model selection.
runCVGMF	Perform a stochastic gradient descent generalized matrix factorization (sgdGMF) on cells, based on the expression or mass spectrometry data in a SingleCellExperiment, SummarizedExperiment or QFeatures object.
runCVGMF-method	Perform a stochastic gradient descent generalized matrix factorization (sgdGMF) on cells, based on the expression or mass spectrometry data in a SingleCellExperiment, SummarizedExperiment or QFeatures object.
runGMF	Perform a stochastic gradient descent generalized matrix factorization (sgdGMF) on cells or bulk samples, based on the expression or mass spectrometry data in a SingleCellExperiment, SummarizedExperiment or QFeatures object.
runGMF-method	Perform a stochastic gradient descent generalized matrix factorization (sgdGMF) on cells or bulk samples, based on the expression or mass spectrometry data in a SingleCellExperiment, SummarizedExperiment or QFeatures object.
runRankGMF	Perform an eigendecomposition for model selection based on a screeplot.
runRankGMF-method	Perform an eigendecomposition for model selection based on a screeplot.
screeplot_rank	Functions to create a scree plot for model selection.
screeplot_rank-method	Functions to create a scree plot for model selection.