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

Description Usage Arguments Details Value Fields Examples

The main class used by the BrainSABER package to hold single cell expression data, relevant gene data, and similarity matrices. CellScabbard extends the [SummarizedExperiment::SummarizedExperiment-class] class.

CellScabbard(
  exprsData,
  phenoData = NULL,
  featureData = NULL,
  AIBSARNA = NULL,
  autoTrim = TRUE
)

`exprsData`	expression data matrix for an experiment
`phenoData`	a data frame containing attributes of individual cells
`featureData`	a data frame containing attributes of features (e.g. genes)
`AIBSARNA`	an instance of the AIBSARNA dataset, built using the `buildAIBSARNA()` function
`autoTrim`	If TRUE (default), automatically trim user data to match AIBSARNA using the column names of AIBSARNA and featureData (or rownames of exprsData, if featureData is not supplied) which produce the most matched identifiers. Also automatically fills the relevantGenes slot, using the same column names. The column names are stored in the dataSetId and AIBSARNAid slots.

This class is initialized from a matrix of gene expression values and associated metadata. Methods that operate on CellScabbard objects comprise the BrainSABER workflow.

a new CellScabbard object

dataSetId: A character vector of length 1, containing the column name of the user's data used to trim the data to match AIBSARNA.
AIBSARNAid: A character vector of length 1, containing the column name of AIBSARNA used to trim AIBSARNA to match the user's data
relevantGenes: A [SummarizedExperiment::SummarizedExperiment-class] containing a subset of data from AIBSARNA. Generated by the BrainSABER workflow.
similarityScores: A data.frame containing similarity scores. Generated by the BrainSABER workflow.
similarityDFs: A list containing similarity data frames with age, structure, and similarity scores sorted in decreasing order. Generated by the BrainSABER workflow.
similarityMatrices: A [SummarizedExperiment::Assays-class] object containing similarity matrices, with identical dimensions, for each sample in phenoData. Generated by the BrainSABER workflow.
UNDmatrices: A [SummarizedExperiment::Assays-class] object containing identical-dimension UND matrices for each sample in phenoData. Generated by the BrainSABER workflow.

# 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)