Phenotypic EMD for comparison of single-cell samples

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Documentation for package ‘phemd’ version 1.6.0

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aggregateSamples Aggregate expression data from all samples
all_expn_data Single-cell RNA-seq expression data for melanoma samples
all_genes All genes included in (subsampled) melanoma single-cell RNA-seq expression data
assignCellClusterNearestNode Assign cells to a reference cell subtype
batchIDs Accessor function for batch ID for each sample
batchIDs<- Setter function for protein / gene markers
batchIDs<--method Setter function for protein / gene markers
bindSeuratObj Attach 'Seurat' object to 'Phemd' object
celltypeFreqs Accessor function for cell subtype distribution for each sample
celltypeFreqs<- Setter function for protein / gene markers
celltypeFreqs<--method Setter function for protein / gene markers
clusterIndividualSamples Computes cell subtype abundances for each sample
compareSamples Computes EMD distance matrix representing pairwise dissimilarity between samples
createDataObj Create 'Phemd' object
drawColnames45 Rotates heatmap marker labels 45 degrees
embedCells Generate cell-state embedding
gaussianffLocal Models expression data using generalized linear model with Gaussian error
GDM Accessor function for EMD ground distance matrix
GDM<- Setter function for protein / gene markers
GDM<--method Setter function for protein / gene markers
generateGDM Computes ground distance matrix based on cell embedding
getArithmeticCentroids Get arithmetic centroids (coordinates)
getCellYield Gets cell yield of each sample as a table
getSampleCelltypeFreqs Returns cell subtype distribution for each sample as a table
getSampleHistsByCluster Gets cell subtype frequency histograms for each sample by cluster ID
getSampleSizes Retrieve single-cell sample sizes
groupSamples Performs community detection on sample-sample distance matrix to identify groups of similar samples
heatmap_genes Genes to be used when plotting heatmap for melanoma single-cell RNA-seq expression data
identifyCentroids Identify cluster centroids (cell names)
monocleInfo Accessor function for stored Monocle object
monocleInfo<- Setter function for protein / gene markers
monocleInfo<--method Setter function for protein / gene markers
orderCellsMonocle Compute Monocle2 cell state and pseudotime assignments
phateInfo Accessor function for stored phate object
phateInfo<- Setter function for protein / gene markers
phateInfo<--method Setter function for protein / gene markers
Phemd Phemd class
Phemd-class Phemd class
Phemd-method Setter function for protein / gene markers
Phemd-methods Setter function for protein / gene markers
plotCellYield Plot cell yield of each sample as bar plot
plotEmbeddings Plots Monocle2 cell embedding plots
plotGroupedSamplesDmap Plot diffusion map embedding of samples based on distance matrix
plotHeatmaps Plot heatmap of cell subtypes
plotSummaryHistograms Plots cell subtype frequency histograms summarizing each group of samples
pooledCells Accessor function for aggregated cells used for cell subtype definition
pooledCells<- Setter function for protein / gene markers
pooledCells<--method Setter function for protein / gene markers
printClusterAssignments Writes samples to file based on community detection group assignments
rawExpn Accessor function for stored multi-sample raw expression data
rawExpn<- Setter function for protein / gene markers
rawExpn<--method Setter function for protein / gene markers
removeTinySamples Remove samples with too few cells
retrieveRefClusters Retrieve reference cell clusters
selected_genes Genes to be used when performing clustering and trajectory analyses on melanoma single-cell RNA-seq expression data
selectFeatures Perform feature selection on aggregated data
selectMarkers Accessor function for gene/protein markers measured in experiment
selectMarkers<- Setter function for protein / gene markers
selectMarkers<--method Setter function for protein / gene markers
seuratInfo Accessor function for stored Seurat object within Phemd object
seuratInfo<- Setter function for protein / gene markers
seuratInfo<--method Setter function for protein / gene markers
sNames Accessor function for identifiers of all single-cell samples in experiment
snames_data Sample names for melanoma single-cell RNA-seq expression data
subsampledBool Accessor function for whether or not cells were subsampled when aggregated for cell subtype analysis
subsampledBool<- Setter function for protein / gene markers
subsampledBool<--method Setter function for protein / gene markers
subsampledIdx Accessor function for aggregated cells used for cell subtype definition
subsampledIdx<- Setter function for protein / gene markers
subsampledIdx<--method Setter function for protein / gene markers