getExternalVector {BrainSABER} | R Documentation

## getExternalVector

### 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")

[Package BrainSABER version 1.0.0 Index]