CellScabbard-methods {BrainSABER} | R Documentation

## Methods for the CellScabbard class

### Description

These methods operate on CellScabbard objects. They are used to access the results of the BrainSABER workflow stored within a CellScabbard.

### Usage

    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

### Arguments

`cs` | A CellScabbard object
`value` | data type, any of matrix, data.frame,list, or SimpleList

### Value

The contents of a slot of the CellScabbard object

### Examples

    # 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)

[Package BrainSABER version 1.0.0 Index]