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

## Documentation for package ‘SCArray’ version 1.15.1

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

## Help Pages

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