Convert a Seurat object (or RDS/H5Seurat file) to an AnnData object file
ConvertSeuratToAnnData.Rd
Convert a Seurat object (or RDS/H5Seurat file) to an AnnData object file
Examples
# \donttest{
ConvertSeuratToAnnData(SeuratObject::pbmc_small, "/tmp/pbmc_small.h5ad")
#> Registered S3 method overwritten by 'SeuratDisk':
#> method from
#> as.sparse.H5Group Seurat
#> Validating h5Seurat file
#> Adding scale.data from RNA as X
#> Transfering meta.features to var
#> Adding data from RNA as raw
#> Transfering meta.features to raw/var
#> Transfering meta.data to obs
#> Adding dimensional reduction information for pca
#> Adding feature loadings for pca
#> Adding dimensional reduction information for tsne
#> Adding RNA_snn as neighbors
ConvertSeuratToAnnData(SeuratObject::pbmc_small, "/tmp/pbmc_small.g1.h5ad", subset = 'groups == "g1"')
#> Validating h5Seurat file
#> Adding scale.data from RNA as X
#> Transfering meta.features to var
#> Adding data from RNA as raw
#> Transfering meta.features to raw/var
#> Transfering meta.data to obs
#> Adding dimensional reduction information for pca
#> Adding feature loadings for pca
#> Adding dimensional reduction information for tsne
saveRDS(SeuratObject::pbmc_small, "/tmp/pbmc_small.rds")
ConvertSeuratToAnnData("/tmp/pbmc_small.rds", "/tmp/pbmc_small.h5ad")
#> Warning: Key ‘rna_’ taken, using ‘rnav3_’ instead
#> Renaming default assay from RNAv3 to RNA
#> Warning: Key ‘rnav3_’ taken, using ‘rna_’ instead
#> Creating h5Seurat file for version 3.1.5.9900
#> Adding counts for RNA
#> Adding data for RNA
#> Adding scale.data for RNA
#> Adding variable features for RNA
#> Adding feature-level metadata for RNA
#> Adding cell embeddings for pca
#> Adding loadings for pca
#> Adding projected loadings for pca
#> Adding standard deviations for pca
#> Adding JackStraw information for pca
#> Adding cell embeddings for tsne
#> No loadings for tsne
#> No projected loadings for tsne
#> No standard deviations for tsne
#> No JackStraw data for tsne
#> Validating h5Seurat file
#> Adding scale.data from RNA as X
#> Transfering meta.features to var
#> Adding data from RNA as raw
#> Transfering meta.features to raw/var
#> Transfering meta.data to obs
#> Adding dimensional reduction information for pca
#> Adding feature loadings for pca
#> Adding dimensional reduction information for tsne
#> Adding RNA_snn as neighbors
# }