CellScabbard-methods: Methods for the CellScabbard class

In BrainSABER: Brain Span Atlas in Biobase Expressionset R toolset

Description

These methods operate on CellScabbard objects. They are used to access the results of the BrainSABER workflow stored within a CellScabbard.

Usage

dataSetId(cs)

dataSetId(cs) <- value

AIBSARNAid(cs)

AIBSARNAid(cs) <- value

relevantGenes(cs)

relevantGenes(cs) <- value

similarityScores(cs)

similarityScores(cs) <- value

similarityDFs(cs)

similarityDFs(cs) <- value

similarityMatrices(cs)

similarityMatrices(cs) <- value

UNDmatrices(cs)

UNDmatrices(cs) <- value

Arguments

cs	A CellScabbard object
value	data type, any of matrix, data.frame,list, or SimpleList

Value

The contents of a slot of the CellScabbard object

Examples

# construct example data set
AIBSARNA <- buildAIBSARNA(mini = TRUE)

# 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, ]

# construct a CellScabbard data set
myGenes <- CellScabbard(exprsData = exprs, phenoData = pd, featureData = fd, 
                        AIBSARNA = AIBSARNA, autoTrim = TRUE)
relevantGenes(myGenes)

# the following fields will be empty as output must be assigned to 
# them first
similarityScores(myGenes)
similarityMatrices(myGenes)
similarityDFs(myGenes)
UNDmatrices(myGenes)

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