getExternalVector {BrainSABER} | R Documentation |
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
getExternalVector( dataSet, index = 1, AIBSARNA = NULL, dataSetId, AIBSARNAid = c("gene_id", "ensembl_gene_id", "gene_symbol", "entrez_id", "refseq_ids") )
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
|
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" |
a named vector of gene expression values
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")