getSimMatrix {BrainSABER} | R Documentation

## Get Age, Structure Acronym, and Similarity Score Matrix

### Description

This function takes a similarity vector or data frame as returned by `getSimScores` and either a CellScabbard object or a subset of AIBSARNA as returned by `getRelevantGenes`. Returns a numeric matrix or list of matrices of similarity scores with rows labeled by age, and columns labeled by structure_acronym.

### Usage

    getSimMatrix(data = NULL, sim_score = NULL, relevantGenes = NULL)

### Arguments

`data` | a CellScabbard object with non-empty relevantGenes slot
`sim_score` | a vector or data frame of similarity scores
`relevantGenes` | a SummarizedExperiment created using the `getRelevantGenes()` function

### Value

a numeric matrix of similarity scores, or a list of matrices

### Examples

    AIBSARNA <- buildAIBSARNA(mini = TRUE)
    # Example 1 - using CellScabbard class
    # 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, ]
    # build a trimmed data set
    myGenes <- CellScabbard(exprsData = exprs, phenoData = pd, featureData = fd,
                            AIBSARNA = AIBSARNA, autoTrim = TRUE)
    similarityScores(myGenes) <- getSimScores(data = myGenes,
                                              similarity_method = "cosine")
    similarityMatrices(myGenes) <- getSimMatrix(data = myGenes)
    similarityMatrices(myGenes)
    similarityScores(myGenes) <- getSimScores(data = myGenes,
                                              similarity_method = "euclidean")
    similarityMatrices(myGenes) <- getSimMatrix(data = myGenes)
    similarityMatrices(myGenes)

    # Example 2 - manual gene selection and relevant gene extraction
    myGenes <- c(4.484885, 0.121902, 0.510035)
    names(myGenes) <- c("TSPAN6", "DPM1", "C1orf112")
    myGeneSet <- getRelevantGenes(myGenes, AIBSARNA = AIBSARNA,
        AIBSARNAid = "gene_symbol")
    myCosScore <- getSimScores(myGenes, myGeneSet, similarity_method = "cosine")
    myEucScore <- getSimScores(myGenes, myGeneSet,
                               similarity_method = "euclidean")
    myCosineMatrix <- getSimMatrix(sim_score = myCosScore,
                                   relevantGenes = myGeneSet)
    myEuclideanMatrix <- getSimMatrix(sim_score = myEucScore,
                                      relevantGenes = myGeneSet)

[Package BrainSABER version 1.0.0 Index]