getSimMatrix: Get Age, Structure Acronym, and Similarity Score Matrix

In bicbioeng/BrainSABER: Brain Span Atlas in Biobase Expressionset R toolset

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)

bicbioeng/BrainSABER documentation built on Oct. 10, 2021, 6:38 a.m.