exampleData: An example data for the SDAMS package

In Stat-Li/SDAMS: Differential Abundant Analysis for Metabolomics and Proteomics Data

Description

SDAMS package provides two different data formats for prostate cancer proteomics data, which is from the human urinary proteome database(http://mosaiques-diagnostics.de/mosaiques-diagnostics/human-urinary-proteom-database). There are 526 prostate cancer subjects and 1503 healthy subjects. A total of 5605 proteomic features were measured for each subject. For illustration purpose, we took a 10% subsample randomly from this real data. This example data contains 560 proteomic features for 202 experimental subjects with 49 prostate cancer subjects and 153 healthy subjects. exampleSumExp.rda is an object of SummarizedExperiment class which stores the information of both proteomic features and experimental subjects. ProstateFeature.csv contains a matrix-like proteomic feature data and ProstateGroup.csv contains a single column of experimental subject group data.

Usage

  data(exampleSumExp)
  

Value

An object of SummarizedExperiment class.

References

Siwy, J., Mullen, W., Golovko, I., Franke, J., and Zurbig, P. (2011). Human urinary peptide database for multiple disease biomarker discovery. PROTEOMICS-Clinical Applications 5, 367-374.

See Also

SDA

Examples

#------ load data --------
data(exampleSumExp)
exampleSumExp
feature = assay(exampleSumExp) # access feature data
group = colData(exampleSumExp)$grouping # access grouping information
SDA(exampleSumExp)

Stat-Li/SDAMS documentation built on May 26, 2019, 11:58 p.m.