data-raw/makeIntegrations.R

In sherrillmix/vipor: Plot Categorical Data Using Quasirandom Noise and Density Estimates

#http://www.retrovirology.com/content/10/1/90/additional
#something messing up read directly so just download and delete
download.file('https://static-content.springer.com/esm/art%3A10.1186%2F1742-4690-10-90/MediaObjects/12977_2013_3591_MOESM2_ESM.gz','ints.csv.gz')
ints<-read.csv('ints.csv.gz',stringsAsFactors=FALSE)
file.remove('ints.csv.gz')
desiredCols<-c('study'='sample','latent'='isLatent','nearestGene'='logDist_nearest','H4K12ac'='H4K12ac_50000')
integrations<-ints[,desiredCols]
colnames(integrations)<-names(desiredCols)
integrations$latent<-ifelse(integrations$latent,'Unexpressed','Expressed')
integrations$nearestGene<-ifelse(ints$inGene,0,round(exp(integrations$nearestGene)))
integrations$study<-sub(' .*$','',integrations$study)


save(integrations,file='../data/integrations.RData')
tools::resaveRdaFiles('../data/integrations.RData')