getRelevantGenes {BrainSABER} | R Documentation |
This function returns a subset of the AIBSARNA dataset, containing only
the genes in data
, which may be a vector, a SummarizedExperiment
or derivative assay()
and rowData()
, or a CellScabbard.
If a vector is used, it must consist of numerical gene expression values
with names comparable to one column of identifiers present in AIBSARNA.
If data
is a CellScabbard, results are stored in the relevantGenes
slot of the object.
getRelevantGenes( data, dataSetId = NULL, AIBSARNA = NULL, AIBSARNAid = c("gene_id", "ensembl_gene_id", "gene_symbol", "entrez_id", "refseq_ids") )
data |
a vector of named gene expression values, or a compatible data set |
dataSetId |
(Optional) If |
AIBSARNA |
an instance of the AIBSARNA dataset, built using the
|
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 SummarizedExperiment consisting of genes in data
, sorted
to match the order of the genes in data
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) relevantGenes(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")