examdata_degs: Differential expressed genes used in examples

In DanWiebe/FoldGO: Package for Fold-specific GO Terms Recognition

Description

We used two datasets in examples:

1. RNA-seq experiment on auxin treatment of Arabidopsis thaliana roots (degenes)

2. RNA-seq experiment on mRNA differential expression in LNCaP cells expressing the wild-type androgen receptor (AR-WT) or the ligand-independent AR-V7 splice variant (degenes_hum)

Usage

degenes

degenes_hum

Format

A dataframes with 4 variables and 789 and 2079 for A. thaliana and H. sapiens correspondingly, where colnames are:

GeneID

Gene identifier

FC

fold-change value

pval

p-value

qval

Benjamini-Yekutieli adjusted p-value

Source

1. A. thaliana and auxin: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97258

2. H. sapiens LNCap AR-V7: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71334

Examples

# load degenes from RNA-seq experiment on auxin treatment of Arabidopsis thaliana roots
data("degenes")

DanWiebe/FoldGO documentation built on May 1, 2020, 11:02 p.m.