exportCdt: Functions to generate fTreeView files

In uc-bd2k/gimmR: This package was built to cluster gene expression data using the Gaussian Infinite Mixture Model.

Description

exportCdt, exportGtr, exportAtr, are slightly modified of the r2cdt, r2gtr, and r2atr functions, respectively, from the package ctc.

exportCdt generates a tab-delimited cdt file from a dataframe where the first column contains gene IDs, the second column contains gene names or descriptions, and the remaining columns represent samples. Column names are assumed to be sample names. In addition, corresponding hierarchical gene and sample clusterings are required to re-order genes and samples accordingly.

exportGtr and exportAtr generate tab-delimited TreeView files representing the hierarchical gene and sample clustering, respectively.

Usage

exportCdt(hr, hc, data, labels = TRUE, description = TRUE, file = "cluster.cdt", dec = ".")
exportGtr(hr, file = "cluster.gtr", dec = ".")
exportAtr(hc, file = "cluster.atr", dec = ".")

Arguments

hr	An hclust object representing the gene clustering
hc	An hclust object representing the sample clustering
data	A dataframe where the first column may contain gene IDs, the second column may contain gene names or descriptions, and the remaining columns represent samples. Column names are assumed to be sample names.
labels	If TRUE, the first column of data is assumed to contain gene IDs.
description	If TRUE, the second column of data is assumed to contain gene names or descriptions.
file	The name of the file to be generated.
dec	The character to be used for decimal points.

Value

Nothing is returned but a file with the specified name is created.

Author(s)

Johannes Freudenberg

References

ctc package: http://antoinelucas.free.fr/ctc/

fTreeView: http://eh3.uc.edu/ftreeview

See Also

ctc, hclust

Examples

data(GalData)
gimmOut <- runGimmNPosthoc(GalData, dataFile="galData", M=20, T=820, estimate_contexts="y", intFiles=TRUE, verbose=TRUE)
exportCdt(gimmOut$hGClustData, gimmOut$hSClustData, gimmOut$clustData)
exportGtr(gimmOut$hGClustData)
exportAtr(gimmOut$hSClustData)

uc-bd2k/gimmR documentation built on May 3, 2019, 2:15 p.m.