RTN (version 1.10.0)

RTN.data: A pre-processed dataset for the RTN package.

Description

A minimum dataset used to demonstrate RTN main functions.

Usage

data(dt4rtn)

Format

dt4rtn List containing 6 R objects: 'gexp', 'gexpIDs', 'pheno', 'phenoIDs', 'hits' and 'tfs'.

Details

The dataset consists of 6 R objects used in the RTN vignettes. It should be regarded as a toy example for demonstration purposes only, despite being extracted, pre-processed and size-reduced from Fletcher et al. (2012) and Curtis et al. (2012).

dt4rtn$gexp

a named gene expression matrix with 50 samples (reduced for demonstration purposes only).

dt4rtn$gexpIDs

a data.frame of characters with probe ids matching a secundary annotation source (e.g. Probe-to-ENTREZ).

dt4rtn$pheno

a named numeric vector with differential gene expression data.

dt4rtn$phenoIDs

a data.frame of characters with probe ids matching a secundary annotation source (e.g. Probe-to-ENTREZ).

dt4rtn$hits

a character vector with genes differentially expressed.

dt4rtn$tfs

a named vector with transcriptions factors.

References

Fletcher M.N.C. et al., Master regulators of FGFR2 signalling and breast cancer risk. Journal Paper (in preparation), 2012.

Curtis C. et al., The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 7403. 2012.

Examples

    data(dt4rtn)