Multi-subject single cell deconvolution

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Documentation for package ‘MuSiC’ version 0.2.0

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Abs_diff_multi Plot heatmap of Absolute difference between estimated and real cell type proportions
Anova_info ANOVA Test for each gene
Boxplot_Est Boxplot of estimated cell type proportions
bulk_construct Construct artificial bulk tissue expression from single cell data
CellTotal.df Compare cell type specific total expression (library size) between 2 dataset
Eval_multi Evaluate estimation methods
fpkmToTpm Calculate fpkm to tpm
get_upper_tri Get upper triangle matrix
Jitter_Est Jitter plot of estimated cell type proportions
music.basic Estimate cell type proportion with MuSiC and NNLS
music.basic.ct Estimate cell type proportion with MuSiC and NNLS
music.iter Scaling bulk data and signature matrix and estimate cell type proportion
music.iter.ct Scaling bulk data and signature matrix and estimate cell type proportion
music_basis Prepare Design matrix and Cross-subject Variance for MuSiC Deconvolution
music_Design.matrix Cell type specific library size
music_M.theta Cross-subject Mean of Relative Abundance
music_prop MuSiC Deconvolution
music_prop.cluster MuSiC Deconvolution with Clusters
music_S Cell type specific library size
music_Sigma Cross-subject Varirance of Relative Abundance
music_Sigma.ct Cross-subject Corvriance of Relative Abundance
music_Theta Subject and cell type specific relative abundance
my.log log transformation with regulation
my.rowMeans Calcuate Row Means with NA remove
my.sqrt Calculate square root of all values
plotCellTotal.two Plot the cell type specific library size of 2 single cell datasets
Prop_comp_multi Plot heatmap of real and estimated cell type proportions
Prop_convert Convert list of real and estimated cell type proportions to data frame
Prop_heat_Est Heatmap of estimated cell type proportions
relative.ab Calculate relative abundance
Relative_gene_boxplot Boxplot of relative abundance
Scatter_multi Plot Scatter plot of real and estimated cell type proportions
Twocelltype.Generator Simulate Single cell read counts
weight.cal.ct Calculate weight with cross cell type covariance
Weight_cal Calculate weight with cross-subject variance for each cell types