getSimDataFrame {BrainSABER} | R Documentation |
This function takes in a CellScabbard object, or both a similarity vector
or data frame as returned by getSimScores
and a subset of AIBSARNA
as returned by getRelevantGenes
. Constructs a data.frame
with columns age, structure_acroynym, and either cosine_similarity or
euclidean_similarity, sorted by similarity score in decreasing order.
In the case of a similarity data frame, a list of data frames is returned.
getSimDataFrame( data = NULL, sim_score = NULL, relevantGenes = NULL, similarity_method = "cosine" )
data |
a CellScabbard object with non-empty relevantGenes and
similarityScores slots, or a SummarizedExperiment created using the
|
sim_score |
a vector or data frame of similarity scores |
relevantGenes |
a SummarizedExperiment object created using the
|
similarity_method |
currently supported similarity methods are "cosine" and "euclidean", defaults to "cosine" |
a three-column data.frame or list of data frames
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) # cosine similarity method similarityScores(myGenes) <- getSimScores(data = myGenes, similarity_method = "cosine") similarityDFs(myGenes) <- getSimDataFrame(data = myGenes, similarity_method = "cosine") similarityDFs(myGenes) # euclidean similarity method similarityScores(myGenes) <- getSimScores(data = myGenes, similarity_method = "euclidean") similarityDFs(myGenes) <- getSimDataFrame(data = myGenes, similarity_method = "euclidean") similarityDFs(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, relevantGenes = myGeneSet, similarity_method = "cosine") myEucScore <- getSimScores(myGenes, relevantGenes = myGeneSet, similarity_method = "euclidean") myCosineDF <- getSimDataFrame(sim_score = myCosScore, relevantGenes = myGeneSet, similarity_method = "cosine") myEuclideanDF <- getSimDataFrame(sim_score = myEucScore, relevantGenes = myGeneSet, similarity_method = "euclidean")