Man pages for yavorska/TenXAnalysisPackage
Analysis of the 10x Genomics 1.3 Million Cells Data

cellCountsReturn cellCounts data.frame
cellCountsExprReturn the total number of genes expressed for each cell
cellCountsTransReturn the total number of transcripts for each cell
cellGroupReturn the cellGroup vector
cellIndexCells in data
cellLibReturn the libraryID vector
cellMouseReturn the mouseID vector
cellNTotal number of cells in the data set
determineGeneFromGOFind genes associated with a GO term
determineGeneFromQueryFind genes containing some query in their GO description
determineGeneIDFind gene name in data
determineGOFromGeneFind GO terms associated with a gene
determineGroupAnnotationsDetermine group annotations
determineLibraryAnnotationsDetermine library annotations
determineLibraryFromGroupGet the library that this group belongs to
determineMouseFromGroupGet the mouse that this group belongs to
determineSampleFromGroupGet indices of cells in a group
EG2GOGO annotation data file
geneCountsReturn geneCounts data.frame
geneENSEMBLReturn the ENSEMBL names of the genes
geneExpressedReturn geneExpressed data.frame
geneIndexGenes in data
geneNTotal number of genes in the data set
geneNamesReturn the HGNC names of the genes
generateSubsetGenerate a TenXSubset object
generateSummaryExprGenerate a summary counts object
groupNTotal number of groups in the data set
groupSizeSize of summary groups
libNTotal number of libraries in the data set
plotTenXTenXSubset object data summaries
plotTenXGenePlot gene summary for TenXSubset object
plotTenXGeneCorCompare gene expression across multiple genes
plotTenXGeneGOPlot GO summary for specified gene set
plotTenXGenePairCompare gene expression profiles for two genes
plotTenXGOPlot GO summary for TenXSubset object
plotTenXGroupExprPlot how gene expression changes based on library
plotTenXMouseExprPlot how gene expression changes based on mouse
TenXse_colDatacolData of the original data set
TenXse_rowDatarowData of the original data set
TenXSubsetAllSummary file for entire data set
TenXSubset-classClass used to represent the grouped TenXData. The object...
yavorska/TenXAnalysisPackage documentation built on Aug. 10, 2017, 12:04 a.m.