ABCGCB: Classification of cell of origin

In oncoclass/hemaClass: One-by-one normalization and classification of hematological malignacies

Description

Classification of DLBCL samples according to the ABC/GCB classifier.

Usage

ABCGCB(new.data, NC.range = c(0.1, 0.9))

Arguments

new.data	An expression matrix.
NC.range	A numeric vector with values for which the probabilities should be cut.

Details

The function ABC/GCB classifies DLBCL patients according to the cell of origin for the tumor.

Value

A list of probabilities and classes regarding each patients association with the classes.

Author(s)

Steffen Falgreen <sfl (at) rn.dk>
Anders Ellern Bilgrau <abilgrau (at) math.aau.dk>

References

Reference to the ABC/GCB and hemaClass paper.

Examples

files <- dir(system.file("extdata/celfiles", package = "hemaClass"),
             full.names = TRUE)
affyBatch <- readCelfiles(filenames = files)

# The cel files are pre-processed
affyRMA <- rmaPreprocessing(affyBatch)

# The function rmaPreprocessing returns median centered and scaled
# expression values in the slot exprs.sc.

# The slot exprs.sc.mean contains mean cetered and scaled expression values.
# This scaling can also be achieved using the function microarrayScale.
affyRMA.sc <- microarrayScale(affyRMA$exprs, center = "median")

# We may now use the ABCGCB classifier
ABCGCB(affyRMA.sc)

oncoclass/hemaClass documentation built on May 24, 2019, 2:19 p.m.