# Subset using the `[` operator. Apply the `[` operator to an `ondisc_matrix`, `metadata_ondisc_matrix`, or `multimodal_ondisc_matrix` to subset the object. You can pass logical, character, or numeric vectors to `[`; character vectors are assumed to refer to feature IDs (for rows) and cell barcodes (for columns). ```r ## S4 method for signature 'ondisc_matrix,missing,missing,missing' x[i, j, drop] ## S4 method for signature 'ondisc_matrix,ANY,missing,missing' x[i, j] ## S4 method for signature 'ondisc_matrix,missing,ANY,missing' x[i, j] ## S4 method for signature 'ondisc_matrix,ANY,ANY,missing' x[i, j] ## S4 method for signature 'metadata_ondisc_matrix,ANY,ANY,missing' x[i, j, drop] ## S4 method for signature 'metadata_ondisc_matrix,ANY,missing,missing' x[i, j, drop] ## S4 method for signature 'metadata_ondisc_matrix,missing,ANY,missing' x[i, j, drop] ## S4 method for signature 'metadata_ondisc_matrix,missing,missing,missing' x[i, j, drop] ## S4 method for signature 'multimodal_ondisc_matrix,missing,missing,missing' x[i, j, drop] ## S4 method for signature 'multimodal_ondisc_matrix,missing,ANY,missing' x[i, j, drop] ## S4 method for signature 'multimodal_ondisc_matrix,ANY,ANY,ANY' x[i, j, drop] ``` ## Arguments - `x`: an `ondisc_matrix`, `metadata_ondisc_matrix`, or `multimodal_ondisc_matrix` object. - `i`: a vector (numeric, logical, or character) indicating features to keep. - `j`: a vector (numeric, logical, or character) indicating cells to keep. - `drop`: not used ## Returns An appropriately subset object of the same class as `x`. ## Details You can subset an `ondisc_matrix` and a `metadata_ondisc_matrix` by cell and/or feature. You can subset a `multimodal_ondisc_matrix` by cell only (because the features differ across modalities). ## Examples ```r # NOTE: You must create the RDS files "expressions.rds" and # "perturbations.rds" to run this example. Navigate to the help file of # "create_ondisc_matrix_from_mtx" (via ?create_ondisc_matrix_from_mtx), # and execute both code blocks. # subset an ondisc_matrix h5_fp <- paste0(tempdir(), "/expressions.h5") if (file.exists(h5_fp)) { odm <- ondisc_matrix(h5_file = h5_fp) # keep cells 100-110 x <- odm[,100:110] # keep all cells except 50, 100, 150 x <- odm[,-c(50, 100, 150)] # keep genes ENSG00000188305, ENSG00000257284, and ENSG00000251655: x <- odm[c("ENSG00000188305", "ENSG00000257284", "ENSG00000251655"),] # keep the cells CTTAGGACACTGGCGT-1 and AAAGGATTCACATCAG-1: x <- odm[,c("CTTAGGACACTGGCGT-1", "AAAGGATTCACATCAG-1")] # keep all genes except ENSG00000188305 and ENSG00000257284 x <- odm[!(get_feature_ids(odm) %in% c("ENSG00000188305", "ENSG00000257284")),] } # subset a metadata_ondic_matrix expressions_fp <- paste0(tempdir(), "/expressions.rds") if (file.exists(expressions_fp)) { expressions <- readRDS(expressions_fp) # keep cells 100-110 x <- expressions[,100:110] # keep genes ENSG00000188305, ENSG00000257284, and ENSG00000251655 x <- expressions[c("ENSG00000188305", "ENSG00000257284", "ENSG00000251655"),] } # subset a multimodal ondisc_matrix expression_fp <- paste0(tempdir(), "/expressions.rds") perturbations_fp <- paste0(tempdir(), "/perturbations.rds") if (file.exists(expression_fp) && file.exists(perturbations_fp)) { expressions <- readRDS(expression_fp) perturbations <- readRDS(expression_fp) crispr_experiment <- multimodal_ondisc_matrix(list(expressions = expressions, perturbations = perturbations)) # Keep all cells except 10,100, and 105. x <- crispr_experiment[,-c(10,100,105)] # Keep the first 5 cells x <- crispr_experiment[,1:5] } ```

subset-odm function