Man pages for phemd
Phenotypic EMD for comparison of single-cell samples

aggregateSamplesAggregate expression data from all samples
all_expn_dataSingle-cell RNA-seq expression data for melanoma samples
all_genesAll genes included in (subsampled) melanoma single-cell...
assignCellClusterNearestNodeAssign cells to a reference cell subtype
batchIDsAccessor function for batch ID for each sample
bindSeuratObjAttach 'seurat' object to 'Phemd' object
celltypeFreqsAccessor function for cell subtype distribution for each...
clusterIndividualSamplesComputes cell subtype abundances for each sample
compareSamplesComputes EMD distance matrix representing pairwise...
createDataObjCreate 'Phemd' object
drawColnames45Rotates heatmap marker labels 45 degrees
embedCellsGenerate Monocle2 embedding
gaussianffLocalModels expression data using generalized linear model with...
GDMAccessor function for EMD ground distance matrix
generateGDMComputes ground distance matrix based on cell embedding
getArithmeticCentroidsGet arithmetic centroids (coordinates)
getCellYieldGets cell yield of each sample as a table
getSampleCelltypeFreqsReturns cell subtype distribution for each sample as a table
getSampleHistsByClusterGets cell subtype frequency histograms for each sample by...
getSampleSizesRetrieve single-cell sample sizes
groupSamplesPerforms community detection on sample-sample distance matrix
heatmap_genesGenes to be used when plotting heatmap for melanoma...
identifyCentroidsIdentify cluster centroids (cell names)
monocleInfoAccessor function for stored Monocle object
orderCellsMonocleCompute Monocle2 cell state and pseudotime assignments
PhemdPhemd class
Phemd-methodsSetter function for protein / gene markers
plotCellYieldPlot cell yield of each sample as bar plot
plotEmbeddingsPlots Monocle2 cell embedding plots
plotGroupedSamplesDmapPlot diffusion map embedding of samples based on distance...
plotHeatmapsPlot heatmap of cell subtypes
plotSummaryHistogramsPlots cell subtype frequency histograms summarizing each...
pooledCellsAccessor function for aggregated cells used for cell subtype...
printClusterAssignmentsWrites samples to file based on community detection group...
rawExpnAccessor function for stored multi-sample raw expression data
removeTinySamplesRemove samples with too few cells
retrieveRefClustersRetrieve reference cell clusters
selected_genesGenes to be used when performing clustering and trajectory...
selectFeaturesPerform feature selection on aggregated data
selectMarkersAccessor function for gene/protein markers measured in...
seuratInfoAccessor function for stored Seurat object within Phemd...
sNamesAccessor function for identifiers of all single-cell samples...
snames_dataSample names for melanoma single-cell RNA-seq expression data
subsampledBoolAccessor function for whether or not cells were subsampled...
subsampledIdxAccessor function for aggregated cells used for cell subtype...
phemd documentation built on May 10, 2019, 2:01 a.m.