demo.data {pathview} | R Documentation

## Data for demo purpose

### Description

demo.paths includes pathway ids and optimal plotting parameters when calling pathview.

GSE16873 is a breast cancer study (Emery et al, 2009) downloaded from Gene Expression Omnibus (GEO). Dataset gse16873 is pre-processed using FARMS method and includes 6 patient cases, each with HN (histologically normal) and DCIS (ductal carcinoma in situ) RMA samples. The same dataset is also used in `gage` package. Dataset gse16873.d includes the gene expression changes of two pairs of DCIS vs HN samples.

paths.hsa includes the full list of human pathway ID/names from KEGG.

### Usage

    data(demo.paths)
    data(gse16873.d)
    data(paths.hsa)

### Format

demo.paths is a named list with ids and plotting parameters for 3 pathways. For details do:

`data(demo.paths); demo.paths`

gse16873.d is a numeric matrix with over 10000 rows (genes) and 2 columns (samples). For details do: `data(gse16873.d); str(gse16873.d)`.

paths.hsa is a named vector mapping KEGG pathway ID to human pathway names.

### Source

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16873

[Package pathview version 1.20.0 Index]