getExternalVector: getExternalVector

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

Description

Get a named vector of gene expression values from a single sample in an outside SummarizedExperiment, for use in creating subsets of AIBSARNA with getRelevantGenes and comparison with that subset with getSimScores

Usage

getExternalVector(
  dataSet,
  index = 1,
  AIBSARNA = NULL,
  dataSetId,
  AIBSARNAid = c("gene_id", "ensembl_gene_id", "gene_symbol", "entrez_id",
    "refseq_ids")
)

Arguments

dataSet	a CellScabbard or SummarizedExperiment object
index	the integer index of the sample of dataSet to be used
AIBSARNA	an instance of the AIBSARNA dataset, built using the buildAIBSARNA() function
dataSetId	the name of the column of gene identifiers in rowData(dataSet) to be used to compare dataSet to AIBSARNA.
AIBSARNAid	the name of the column of rowData(AIBSARNA) that is comparable to dataSetId. One of "gene_id", "ensembl_gene_id", "gene_symbol", "entrez_id", "refseq_ids"

Value

a named vector of gene expression values

Examples

miniAIBSARNA <- buildAIBSARNA(mini = TRUE)
myGenes <- c(4.484885, 0.121902, 0.510035)
names(myGenes) <- c("TSPAN6", "DPM1", "C1orf112")
myGeneSet <- getRelevantGenes(myGenes, "gene_symbol", miniAIBSARNA,
    AIBSARNAid = "gene_symbol")
myGeneSampleVector <- getExternalVector(myGeneSet, index = 1, miniAIBSARNA,
    dataSetId = "gene_symbol", AIBSARNAid = "gene_symbol")

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