OpenCyto Analysis of HVTN080 Broken

[tobiguennel]

I tried to re-create some of the anlayses for the HVTN080 (HIV Vaccine Clinical Trial Data) listed at http://opencyto.org/index.html. The analyes do not seem to run appropriately at multiple places most likely due to recent updates:

A specific example is the following code at http://opencyto.org/gatingsets.html:

base.dir<- '/data'
int.data.dir <- file.path(base.dir,'data','HVTN080_demo')
if(!file.exists(int.data.dir)) dir.create(int.data.dir,recursive = TRUE)
res.dir <- file.path(base.dir,'results','HVTN080_demo')
if(!file.exists(int.data.dir)) dir.create(res.dir,recursive = TRUE)
if(!file.exists(file.path(int.data.dir,'gs_manual_clean'))) dir.create(file.path(int.data.dir,'gs_manual_clean'))
if(!file.exists(file.path(int.data.dir,'gs_auto_clean'))) dir.create(file.path(int.data.dir,'gs_auto_clean'))
if(!file.exists(file.path(int.data.dir,'gs_manual_clean','file30612c5fd169.nc'))) download.file('https://www.dropbox.com/sh/y4mxysgioqwxme0/AAAHovWLmmQQeXsbJYoBSZH0a/file30612c5fd169.nc?dl=1',file.path(int.data.dir,'gs_manual_clean','file30612c5fd169.nc'))
if(!file.exists(file.path(int.data.dir,'gs_manual_clean','A3ymadBQH8.dat'))) download.file('https://www.dropbox.com/sh/y4mxysgioqwxme0/AADvlFuBtMKd0vPsf74FFNpKa/A3ymadBQH8.dat?dl=1',file.path(int.data.dir,'gs_manual_clean','A3ymadBQH8.dat'))
if(!file.exists(file.path(int.data.dir,'gs_manual_clean','A3ymadBQH8.rds'))) download.file('https://www.dropbox.com/sh/y4mxysgioqwxme0/AAA9PmCKqY1IIGhvMqMVs40ha/A3ymadBQH8.rds?dl=1',file.path(int.data.dir,'gs_manual_clean','A3ymadBQH8.rds'))
if(!file.exists(file.path(int.data.dir,'gs_manual_clean','sQEv50vxX5.dat'))) download.file('https://www.dropbox.com/sh/oovsrq6ltku1t1h/AACe-eFFVjewkUdUXxEcO7WGa/sQEv50vxX5.dat?dl=1',file.path(int.data.dir,'gs_auto_clean','sQEv50vxX5.dat'))
if(!file.exists(file.path(int.data.dir,'gs_manual_clean','sQEv50vxX5.rds'))) download.file('https://www.dropbox.com/sh/oovsrq6ltku1t1h/AACS3mksbsg5bRXhc0ecIy90a/sQEv50vxX5.rds?dl=1',file.path(int.data.dir,'gs_auto_clean','sQEv50vxX5.rds'))
if(!file.exists(file.path(int.data.dir,'gs_manual_clean','file30614105df5f.nc'))) download.file('https://www.dropbox.com/sh/oovsrq6ltku1t1h/AACT1Bfs2TvH4imJRPCbg9fQa/file30614105df5f.nc?dl=1',file.path(int.data.dir,'gs_auto_clean','file30614105df5f.nc'))

auto<-load_gs(file.path(int.data.dir,'gs_auto_clean'))
manual<-load_gs(file.path(int.data.dir,'gs_auto_clean'))

auto_stats<-getPopStats(auto,statistic="count")
cd8_auto<-COMPASSContainerFromGatingSet(gs=auto,node="8\\+$",individual_id="PTID",sample_id="name",markers=c("IFNg","TNFa","IL2","Granzyme B","Perforin"))

The error messge is:

Another issue is that PTID should be pub_id in the function call.