exampleData: Two example datasets for SDAMS package

In SDAMS: Differential Abundant Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data

Description

SDAMS package provides two types of example datasets: one is prostate cancer proteomics data from mass spectrometry and the other one is single-cell RNA sequencing data.

1. For prostate cancer proteomics data, it 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. SDAMS package provides two different kinds of data formats for prostate cancer proteomics data. 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.

2. For single cell RNA sequencing data, it is in the form of transcripts per kilobase million (TPM). The count data can be found at Gene Expression Omnibus (GEO) database with Accession No. GSE29087. There are 92 single cells (48 mouse embryonic stem (ES) cells and 44 mouse embryonic fibroblasts (MEF)) that were analyzed. The example data provided by SDAMS contains 10% of genes which are randomly sampled from the raw dataset. exampleSingleCell.rda is an object of SummarizedExperiment class which stores the information of both gene expression and cell information.

Usage

  data(exampleSumExp)
  data(exampleSingleCell)
  

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.

Islam, S., Kjallquist, U., Moliner, A., Zajac, P., Fan, J. B., Lonnerberg, P., & Linnarsson, S. (2011). Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome research, 21(7), 1160-1167.

See Also

SDA

Examples

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

SDAMS documentation built on Nov. 8, 2020, 6:10 p.m.