pigengene: An object of class 'Pigengene'

In Pigengene: Infers biological signatures from gene expression data

Description

This is a toy example object of class pigengene-class. It is used in examples of Pigengene-package. Gene expression profile of 202 acute myeloid leukemia (AML) cases from Mills et al. study. The profile was compared with the profile of 164 myelodysplastic syndromes (MDS) cases and only the 1000 most differentially expressed genes are included.

Usage

data("aml")

Format

An object of pigengene-class.

Details

The object is made using compute.pigengene fucntion from aml and mds data as shown in the examples. The R CMD build --resave-data trick was used to reduce the size of saved object from 3.1 MB to 1.4 MB.

Value

It is an object of pigengene-class.

Source

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15061

References

Mills, Ken I., et al. (2009). Microarray-based classifiers and prognosis models identify subgroups with distinct clinical outcomes and high risk of AML transformation of myelodysplastic syndrome. Blood 114.5: 1063-1072.

See Also

Pigengene-package, pigengene-class, one.step.pigengene, mds, aml, compute.pigengene

Examples

library(pheatmap)
data(pigengene)
plot(pigengene,fontsize=12)

## To reproduce:
data(aml)
data(mds)
data(eigengenes33)
d1 <- rbind(aml,mds)
Labels <- c(rep("AML",nrow(aml)),rep("MDS",nrow(mds)))
names(Labels) <- rownames(d1)
modules33 <- eigengenes33$modules[colnames(d1)]
## Computing:
computed <- compute.pigengene(Data=d1, Labels=Labels, modules=modules33,
   saveFile="pigengene.RData", doPlot=FALSE, verbose=3)
class(computed)
plot(computed, fontsize=12, main="Reproduced")

Pigengene documentation built on Nov. 8, 2020, 6:47 p.m.