Large-scale single-cell omics data manipulation with GDS files

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Documentation for package ‘SCArray’ version 1.16.0

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

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C D M N O P R S T misc

SCArray-package

Large-scale single-cell omics data manipulation with GDS files

-- C --

colAnyNAs	SC_GDSMatrix row/column summarization
colAnyNAs-method	SC_GDSMatrix row/column summarization
colAvgsPerRowSet	SC_GDSMatrix row/column summarization
colAvgsPerRowSet-method	SC_GDSMatrix row/column summarization
colCollapse	SC_GDSMatrix row/column summarization
colCollapse-method	SC_GDSMatrix row/column summarization
colDiffs	SC_GDSMatrix row/column summarization
colDiffs-method	SC_GDSMatrix row/column summarization
colLogSumExps	SC_GDSMatrix row/column summarization
colLogSumExps-method	SC_GDSMatrix row/column summarization
colMaxs	SC_GDSMatrix row/column summarization
colMaxs-method	SC_GDSMatrix row/column summarization
colMeans	SC_GDSMatrix row/column summarization
colMeans-method	SC_GDSMatrix row/column summarization
colMeans2	SC_GDSMatrix row/column summarization
colMeans2-method	SC_GDSMatrix row/column summarization
colMins	SC_GDSMatrix row/column summarization
colMins-method	SC_GDSMatrix row/column summarization
colProds	SC_GDSMatrix row/column summarization
colProds-method	SC_GDSMatrix row/column summarization
colRanges	SC_GDSMatrix row/column summarization
colRanges-method	SC_GDSMatrix row/column summarization
colSdDiffs	SC_GDSMatrix row/column summarization
colSdDiffs-method	SC_GDSMatrix row/column summarization
colSds	SC_GDSMatrix row/column summarization
colSds-method	SC_GDSMatrix row/column summarization
colsum	SC_GDSMatrix row/column summarization
colsum-method	SC_GDSMatrix row/column summarization
colSums	SC_GDSMatrix row/column summarization
colSums-method	SC_GDSMatrix row/column summarization
colSums2	SC_GDSMatrix row/column summarization
colSums2-method	SC_GDSMatrix row/column summarization
colVarDiffs	SC_GDSMatrix row/column summarization
colVarDiffs-method	SC_GDSMatrix row/column summarization
colVars	SC_GDSMatrix row/column summarization
colVars-method	SC_GDSMatrix row/column summarization
colWeightedMeans	SC_GDSMatrix row/column summarization
colWeightedMeans-method	SC_GDSMatrix row/column summarization
colWeightedSds	SC_GDSMatrix row/column summarization
colWeightedSds-method	SC_GDSMatrix row/column summarization
colWeightedVars	SC_GDSMatrix row/column summarization
colWeightedVars-method	SC_GDSMatrix row/column summarization
col_nnzero	Numbers of Non-zeros
col_nnzero-method	Numbers of Non-zeros
crossprod	SC_GDSArray subsetting, Ops, Math
crossprod-method	SC_GDSArray subsetting, Ops, Math

-- D --

dimnames<-	SC_GDSArray subsetting, Ops, Math
dimnames<--method	SC_GDSArray subsetting, Ops, Math

-- M --

Math	SC_GDSArray subsetting, Ops, Math
Math-method	SC_GDSArray subsetting, Ops, Math

-- N --

names<-	SC_GDSArray subsetting, Ops, Math
names<--method	SC_GDSArray subsetting, Ops, Math

-- O --

Ops	SC_GDSArray subsetting, Ops, Math
Ops-method	SC_GDSArray subsetting, Ops, Math

-- P --

pmax2	SC_GDSArray subsetting, Ops, Math
pmax2-method	SC_GDSArray subsetting, Ops, Math
pmin2	SC_GDSArray subsetting, Ops, Math
pmin2-method	SC_GDSArray subsetting, Ops, Math

-- R --

rowAnyNAs	SC_GDSMatrix row/column summarization
rowAnyNAs-method	SC_GDSMatrix row/column summarization
rowAvgsPerColSet	SC_GDSMatrix row/column summarization
rowAvgsPerColSet-method	SC_GDSMatrix row/column summarization
rowCollapse	SC_GDSMatrix row/column summarization
rowCollapse-method	SC_GDSMatrix row/column summarization
rowDiffs	SC_GDSMatrix row/column summarization
rowDiffs-method	SC_GDSMatrix row/column summarization
rowLogSumExps	SC_GDSMatrix row/column summarization
rowLogSumExps-method	SC_GDSMatrix row/column summarization
rowMaxs	SC_GDSMatrix row/column summarization
rowMaxs-method	SC_GDSMatrix row/column summarization
rowMeans	SC_GDSMatrix row/column summarization
rowMeans-method	SC_GDSMatrix row/column summarization
rowMeans2	SC_GDSMatrix row/column summarization
rowMeans2-method	SC_GDSMatrix row/column summarization
rowMins	SC_GDSMatrix row/column summarization
rowMins-method	SC_GDSMatrix row/column summarization
rowProds	SC_GDSMatrix row/column summarization
rowProds-method	SC_GDSMatrix row/column summarization
rowRanges	SC_GDSMatrix row/column summarization
rowRanges-method	SC_GDSMatrix row/column summarization
rowSdDiffs	SC_GDSMatrix row/column summarization
rowSdDiffs-method	SC_GDSMatrix row/column summarization
rowSds	SC_GDSMatrix row/column summarization
rowSds-method	SC_GDSMatrix row/column summarization
rowsum	SC_GDSMatrix row/column summarization
rowsum-method	SC_GDSMatrix row/column summarization
rowSums	SC_GDSMatrix row/column summarization
rowSums-method	SC_GDSMatrix row/column summarization
rowSums2	SC_GDSMatrix row/column summarization
rowSums2-method	SC_GDSMatrix row/column summarization
rowVarDiffs	SC_GDSMatrix row/column summarization
rowVarDiffs-method	SC_GDSMatrix row/column summarization
rowVars	SC_GDSMatrix row/column summarization
rowVars-method	SC_GDSMatrix row/column summarization
rowWeightedMeans	SC_GDSMatrix row/column summarization
rowWeightedMeans-method	SC_GDSMatrix row/column summarization
rowWeightedSds	SC_GDSMatrix row/column summarization
rowWeightedSds-method	SC_GDSMatrix row/column summarization
rowWeightedVars	SC_GDSMatrix row/column summarization
rowWeightedVars-method	SC_GDSMatrix row/column summarization
row_nnzero	Numbers of Non-zeros
row_nnzero-method	Numbers of Non-zeros
runPCA	Perform PCA on SC_GDSMatrix and expression data
runPCA-method	Perform PCA on SC_GDSMatrix and expression data

-- S --

scale	SC_GDSArray subsetting, Ops, Math
scale-method	SC_GDSArray subsetting, Ops, Math
SCArray	Large-scale single-cell omics data manipulation with GDS files
scArray	Get an DelayedArray instance
SCArray-classes	Class list defined in SCArray
SCArray-stats	SC_GDSMatrix row/column summarization
SCArray-utils	SC_GDSArray subsetting, Ops, Math
SCArrayFileClass	Class list defined in SCArray
SCArrayFileClass-class	Class list defined in SCArray
scClose	Open/Close a Single-cell GDS File
scColAutoGrid	Automatic grids for matrix-like objects
scColMeanVar	SC_GDSMatrix row/column summarization
scColMeanVar-method	SC_GDSMatrix row/column summarization
scConvGDS	Create a GDS file
scExperiment	Get a SummarizedExperiment
scGetFiles	File names for on-disk backend
scGetFiles-method	File names for on-disk backend
scHDF2GDS	Convert HDF5 files to GDS
scMemory	Load Data to Memory
scMemory-method	Load Data to Memory
scMEX2GDS	Convert MEX files to GDS
scNumSplit	Split a number
scObj	DelayedArray Object in GDS
scOpen	Open/Close a Single-cell GDS File
scReplaceNA	Replacement
scRowAutoGrid	Automatic grids for matrix-like objects
scRowMeanVar	SC_GDSMatrix row/column summarization
scRowMeanVar-method	SC_GDSMatrix row/column summarization
scRunPCA	Perform PCA on SC_GDSMatrix and expression data
scSetBounds	Set the bounds
scSetMax	Set the bounds
scSetMin	Set the bounds
SC_GDSArray	Class list defined in SCArray
SC_GDSArray-class	Class list defined in SCArray
SC_GDSMatrix	Class list defined in SCArray
SC_GDSMatrix-class	Class list defined in SCArray

-- T --

tcrossprod	SC_GDSArray subsetting, Ops, Math
tcrossprod-method	SC_GDSArray subsetting, Ops, Math

-- misc --

%*%	SC_GDSArray subsetting, Ops, Math
%*%-method	SC_GDSArray subsetting, Ops, Math
+	SC_GDSArray subsetting, Ops, Math
+-method	SC_GDSArray subsetting, Ops, Math
-	SC_GDSArray subsetting, Ops, Math
--method	SC_GDSArray subsetting, Ops, Math
[	SC_GDSArray subsetting, Ops, Math
[-method	SC_GDSArray subsetting, Ops, Math
[[	SC_GDSArray subsetting, Ops, Math
[[-method	SC_GDSArray subsetting, Ops, Math