getRelevantGenes: Get a subset of AIBSARNA using a Gene Expression Vector

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

Description

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.

Usage

getRelevantGenes(
  data,
  dataSetId = NULL,
  AIBSARNA = NULL,
  AIBSARNAid = c("gene_id", "ensembl_gene_id", "gene_symbol", "entrez_id",
    "refseq_ids")
)

Arguments

data	a vector of named gene expression values, or a compatible data set
dataSetId	(Optional) If data is not a vector, the name of the column of gene identifiers in rowData(dataSet) to be used to compare data to AIBSARNA.
AIBSARNA	an instance of the AIBSARNA dataset, built using the buildAIBSARNA() function
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 SummarizedExperiment consisting of genes in data, sorted to match the order of the genes in data

Examples

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")

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