CMprep: Pre-process a gene expression dataset for CellMapper

In CellMapper: Predict genes expressed selectively in specific cell types

Description

Prepares a dataset for use with the CMsearch function.

Usage

CMprep(Data, DataSource = '', GeneIDType = '', verbose = TRUE)

Arguments

Data	a numeric matrix or ExpressionSet object containing microarray expression data. The input expression data should be normalized and log-transformed.
DataSource	An optional character vector of length one providing some information about the expression data source.
GeneIDType	An optional character vector of length one that lists the type of gene IDs used in the expression dataset (e.g. "Human Entrez IDs").
verbose	logical value indicating whether progress updates should be provided.

Details

This function calculates the singular value decomposition of a gene expression matrix and prepares the data for use with the CMsearch function. It can take some time for large expression matrices, and so it is recommended to save the output for future use. Pre-processed microarray data, ready for immediate use with CMsearch, can be found in the CellMapperData package.

See the CellMapper vignette for examples about how to use CMprep and associated functions to infer genes selectively expressed in specific cell types.

Value

A 'CellMapperList' object ready to be provided to the CMsearch function.

Author(s)

Brad Nelms

References

B.D. Nelms, L. Waldron, L.A. Barrera, A.W. Weflen, J.A. Goettel, G. Guo, R.K. Montgomery, M.R. Neutra, D.T. Breault, S.B. Snapper, S.H. Orkin, M.L. Bulyk, C. Huttenhower and W.I. Lencer. CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. Genome Biology 2016, 17(1).

See Also

CMsearch, ExpressionSet, CellMapperData

Examples

# Create a mock expression dataset with random expression values
ngenes <- 1000
narrays <- 100
x <- matrix(rnorm(ngenes*narrays), ngenes, narrays)
rownames(x) <- 1:ngenes

# Prepare the dataset for use with CMsearch
data <- CMprep(x)
show(data)

# Save the processed dataset for later
## Not run: 
save(data, file = "Preprocessed_CellMapper_Data.RData")

## End(Not run)

CellMapper documentation built on Nov. 8, 2020, 5:36 p.m.