BAGS: Classification of cell of origin

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

Description

Classification using the B-cell associated gene signatures (BAGS) classifier of Dybkaer et al. [1]. The BAGS classifier attemps to assign the given supplied Diffuse Large B-Cell Lymphomas (DLBCL) samples to one of five classes according to their resembalace to normal Naive (N), Centrocytes (CC), Centroblasts (CB), Memory (M), and Plasmablasts (PB) cells.

Usage

BAGS(new.data, cut.spec = NULL, percent.classified = 85)

Arguments

new.data	An expression matrix.
cut.spec	A numeric value used to threshold the probabilities and determine the class.
percent.classified	A numeric value indicating the percentage of patients that should be classified. An alternative to cut.spec.

Details

The function BAGS classifies DLBCL patients according to the cell of origin for the tumor [1].

Value

A list of probabilities regarding each patients association with each class, the determined class, and the used cut-off thresholds.

Author(s)

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

References

[1] Dybkaer, Karen, Martin Boegsted, Steffen Falgreen, Julie S. Boedker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau et al. "Diffuse large B-cell lymphoma classification system that associates normal B-cell subset phenotypes with prognosis." Journal of Clinical Oncology 33, no. 12 (2015): 1379-1388.

[Add hemaclass.org reference]

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 centered 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
BAGS(affyRMA.sc)

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