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NAMESPACE
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NAMESPACE
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# Native routines that are to be used in R via .Call
useDynLib(SCArray,
c_add, c_get_split,
c_rowSums, c_colSums, c_rowProds, c_colProds,
c_rowMeans, c_rowMeans_final, c_colMeans,
c_rowWMeans, c_rowWMeans_final, c_colWMeans,
c_rowVars, c_rowVars_final, c_colVars,
c_rowWVars, c_rowWVars_final, c_colWVars,
c_rowMeanVar_final, c_colMeanVar,
c_rowMins, c_colMins, c_rowMaxs, c_colMaxs, c_rowRanges, c_colRanges,
c_row_sum_grp, c_col_sum_grp, c_row_nnzero, c_col_nnzero,
c_row_anyNA, c_col_anyNA,
c_rowCollapse_init, c_rowCollapse_done, c_rowCollapse,
c_colCollapse_init, c_colCollapse,
c_sparse_blocksize)
# Export the following names
exportPattern("^sc*")
exportClasses(SCArrayFileClass, SC_GDSArray, SC_GDSMatrix)
exportMethods(
rowSums, colSums, rowSums2, colSums2, rowProds, colProds,
rowMeans, colMeans, rowMeans2, colMeans2,
rowWeightedMeans, colWeightedMeans,
rowVars, colVars, rowSds, colSds,
rowWeightedVars, colWeightedVars, rowWeightedSds, colWeightedSds,
rowMins, colMins, rowMaxs, colMaxs, rowRanges, colRanges,
rowAnyNAs, colAnyNAs, rowCollapse, colCollapse,
row_nnzero, col_nnzero,
colsum, rowsum, scale, pmin2, pmax2
)
# Import all packages listed as Imports or Depends
import(methods)
import(gdsfmt)
import(DelayedArray)
import(DelayedMatrixStats)
importFrom(utils, head, object.size, packageVersion, read.delim, str,
txtProgressBar, setTxtProgressBar)
importFrom(Matrix, crossprod, tcrossprod, nnzero, readMM)
importFrom(S4Vectors, DataFrame, metadata, new2)
importFrom(BiocSingular, bsparam, runPCA)
importFrom(BiocParallel,
bplapply, bpnworkers, bpstart, bpstop, bpisup, SerialParam)
importFrom(SummarizedExperiment, SummarizedExperiment, colData, rowData,
assays, "assays<-", assay, "assay<-")
importFrom(SingleCellExperiment, SingleCellExperiment, altExp,
reducedDim, "reducedDim<-")