barcode {frma} | R Documentation |
This function converts expression values produced via fRMA to a gene expression barcode.
barcode(object, platform=NULL, mu=NULL, tau=NULL, cutoff=6.5, output="binary")
object |
a vector or matrix of expression values or an ExpressionSet or frmaExpressionSet produced by frma |
platform |
the platform of the input data. One of GPL96, GPL570, GPL571, GPL1261, GPL6244, GPL6246. Required if object is a vector or matrix and either mu or tau is NULL. |
mu |
the mean of the unexpressed distribution. If NULL then precomputed values are used if possible. |
tau |
the standard deviation of the unexpressed distribution. If NULL then precomputed values are used if possible. |
cutoff |
the lod score cutoff used if output is binary. |
output |
the desired values to be returned. Options are: p-value, z-score, lod, or binary. |
A matrix containing the type of output specified by the output parameter. The option binary creates a gene expression barcode where 1s denote expressed genes and 0s denote unexpressed genes. The option p-value returns the p-values for the expression values under the unexpressed distribution. The option lod returns the LOD scores for expression values under the unexpressed distribution. The option z-score returns the z-scores for the expression values under the unexpressed distribution.
Matthew N. McCall
library(frma) library(frmaExampleData) data(AffyBatchExample) object <- frma(AffyBatchExample) bc <- barcode(object)