CellScabbard-methods {BrainSABER} | R Documentation |
These methods operate on CellScabbard objects. They are used to access the results of the BrainSABER workflow stored within a CellScabbard.
dataSetId(cs) dataSetId(cs) <- value AIBSARNAid(cs) AIBSARNAid(cs) <- value relevantGenes(cs) relevantGenes(cs) <- value similarityScores(cs) similarityScores(cs) <- value similarityDFs(cs) similarityDFs(cs) <- value similarityMatrices(cs) similarityMatrices(cs) <- value UNDmatrices(cs) UNDmatrices(cs) <- value
cs |
A CellScabbard object |
value |
data type, any of matrix, data.frame,list, or SimpleList |
The contents of a slot of the CellScabbard object
# construct example data set AIBSARNA <- buildAIBSARNA(mini = TRUE) # get a random sample of 3 genes totalGenes <- nrow(AIBSARNA) gene_idx <- sample.int(totalGenes, 3) sample_idx <- c(1,3,5) # Subset AIBSARNA exprs <- assay(AIBSARNA)[gene_idx, sample_idx] fd <- rowData(AIBSARNA)[gene_idx, ] pd <- colData(AIBSARNA)[sample_idx, ] # construct a CellScabbard data set myGenes <- CellScabbard(exprsData = exprs, phenoData = pd, featureData = fd, AIBSARNA = AIBSARNA, autoTrim = TRUE) relevantGenes(myGenes) # the following fields will be empty as output must be assigned to # them first similarityScores(myGenes) similarityMatrices(myGenes) similarityDFs(myGenes) UNDmatrices(myGenes)