getSimScores: Get Similarity Scoring for a Gene Expression Vector

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

Description

This function computes the similarity score of a gene expression vector returned by getExternalVector or a trimmed data set returned by getTrimmedExternalSet, compared to a subset of AIBSARNA, obtained by getRelevantGenes.

Usage

getSimScores(data, relevantGenes = NULL, similarity_method = "cosine")

Arguments

data	a named vector of gene expression values returned by getExternalVector, a SummarizedExperiment returned by getTrimmedExternalSet, or a CellScabbard object.
relevantGenes	a SummarizedExperiment object created using the getRelevantGenes() function
similarity_method	currently supported similarity methods are "cosine" and "euclidean", defaults to "cosine"

Value

If data is a vector, returns a vector of similarity scores for each sample in relevantGenes. If data is a SummarizedExperiment, returns a data frame, with columns containing the similarity scores for and named after each sample in data, and rows named after each sample in relevantGenes. If data is a CellScabbard, the results will be stored in its similarityScores slot.

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")
similarityScores(myGenes)
similarityScores(myGenes) <- getSimScores(data = myGenes,
                                          similarity_method = "euclidean")
similarityScores(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")
CosScores <- getSimScores(myGenes, myGeneSet,
    similarity_method = "cosine")
EucScores <- getSimScores(myGenes, myGeneSet,
    similarity_method = "euclidean")

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