pigengene {Pigengene} | R Documentation

## An object of class `Pigengene`

### 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")

[Package Pigengene version 1.4.20 Index]