getTrimmedExternalSet: Get a trimmed version of an external data set

In BrainSABER: Brain Span Atlas in Biobase Expressionset R toolset

Description

Returns a SummarizedExperiment that is a subset of dataSet containing only genes that are present in AIBSARNA, for use in getSimScores or getUNDmatrix.

Usage

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

Arguments

dataSet	a CellScabbard or SummarizedExperiment object
dataSetId	the name of the column of gene identifiers in rowData(dataSet) to be used to compare dataSet 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 object containing trimmed data set

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)
# use the appropriate id's to extract the trimmed gene set from the data
dataSetId = dataSetId(myGenes)
AIBSARNAid = AIBSARNAid(myGenes)
myTrimmedGeneSet <- getTrimmedExternalSet(myGenes,
    dataSetId = dataSetId, AIBSARNA, AIBSARNAid = AIBSARNAid)

# 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")
myTrimmedGeneSet <- getTrimmedExternalSet(myGeneSet,
    dataSetId = "gene_symbol", AIBSARNA, AIBSARNAid = "gene_symbol")

BrainSABER documentation built on Nov. 8, 2020, 7:28 p.m.