exampleData: Small data set for running examples

In NelleV/moanin: An R Package for Time Course RNASeq Data Analysis

Description

Small data set for running examples

Format

Three objects are loaded, a data frame of expression of 500 genes by 84 samples (testData), a data frame with meta information on those 84 samples (testMeta), and a data frame giving the GOID of the genes in testData.

Details

This data is a subset of the full time course data available as shoemaker2015 and is only provided for the purpose of running examples, and not for biological meaning. Users should refer to the full data set.

The rownames of testData are RefSeq.

Examples

#code used to create data:
## Not run: 
library(timecoursedata)
data(shoemaker2015)
testData<-shoemaker2015$data[1:500,]
whSamples<-which(shoemaker2015$meta$Group %in% c("C","K","M"))
testData<-testData[,whSamples]
testMeta<-droplevels(shoemaker2015$meta[whSamples,])
library(biomaRt)
ensembl = useMart("ensembl")
ensembl = useMart("ensembl")
ensembl = useDataset("mmusculus_gene_ensembl", mart=ensembl)
testGenesGO = getBM(attributes=c("go_id", "refseq_mrna"),
              values=rownames(testData),
              filters="refseq_mrna",
              mart=ensembl)
save(list=c("testData","testMeta","testGenesGO"),file="data/exampleData.rda")

## End(Not run)

NelleV/moanin documentation built on July 28, 2021, 7:34 p.m.