demo.data: Data for demo purpose

In datapplab/pathview: a tool set for pathway based data integration and visualization

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

datapplab/pathview documentation built on March 30, 2024, 9:06 a.m.