Contains embeddings/loadings for contributionGene, as well as phenotype metadata.
DEGAS_seurat
An object of class Seurat with 30084 rows and 2138 columns.
#### Embeddings/loadings
DEGAS_contributionGene <- readRDS("/Desktop/phenome_decomposition/raw_data/DEGAS/contributionGene.rds")#### Metadata
DEGAS_metadata <- read.csv("/Desktop/phenome_decomposition/raw_data/DEGAS/metadata_processed.csv", check.names = FALSE)
colnames(DEGAS_metadata) <- gsub(" ","_",colnames(DEGAS_metadata))
colnames(DEGAS_metadata) <- gsub("[(]|[)]","",colnames(DEGAS_metadata))
rownames(DEGAS_metadata) <- DEGAS_metadata$label_phe_codeempty_mat <- Matrix::sparseMatrix(i = nrow(DEGAS_contributionGene@feature.loadings),
j = nrow(DEGAS_contributionGene@cell.embeddings),
dimnames = list(rownames(DEGAS_contributionGene@feature.loadings),
rownames(DEGAS_contributionGene@cell.embeddings)
)
)
DEGAS_seurat <- Seurat::CreateSeuratObject(counts = empty_mat, assay = "genes", meta.data = DEGAS_metadata)
DEGAS_seurat[["contributionGene"]] <- DEGAS_contributionGene
usethis::use_data(DEGAS_seurat, overwrite = TRUE)
NOTE: The assay data is intentionally filled with an empty sparse matrix due to size limits.