Caprion example

The working directory as with variables is predefined for pilot project on Caprion platform, and we use the appropriate setup for the INTERVAL study.

Our association model is

Execution

The call to the pipeline is made as follows,

local dir : env HPC_WORK
local caprion : env caprion
local y : env y
local trait : env trait
set maxvar 21000
insheet using "`caprion'/data2/phase2.dat", delim(" ") case clear
// To fix the glitch of SNPTEST on covariates
foreach x of varlist PC1-PC20 {
   replace `x'=`x'*10000
}
rename ID_1 id
format id %15.0g
merge 1:1 id using "`dir'/data/interval/interval_data"
gwas2 `trait', studyname(interval) dirgenefiles("`caprion'/data2") chr(19) /*
*/    covariates(agePulse bmi PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 PC11 PC12 PC13 PC14 PC15 PC16 PC17 PC18 PC19 PC20) /*
*/    class(sexPulse ethnicity classification) dirwork("`caprion'/`y'") outfmt(txt)

where the merge command add a variable named sex (0=male, 1=female) as required by the Stata package.

Strangely as before, we need to scale up the principal components (PCs) in order for the model to converge under SNPTEST.

Preparations

export TMPDIR=${HPC_WORK}/work
export dir=~/rda/projects/Caprion_proteomics
export caprion=${dir}/pilot

. /etc/profile.d/modules.sh
module load ceuadmin/stata

  export full=(RCN3_442625488_VADQDGDSMATR RCN3_442666668_EVAKEFDQLTPEESQAR RCN3_All RCN3_DR)
  export abbrev=(RCN3_44262548~R RCN3_44266666~R RCN3_All RCN3_DR)
  for i in {0..3}
  do
    export y=${full[$i]}
    export trait=${abbrev[$i]}
    if [ ! -d ${caprion}/${y} ]; then mkdir ${caprion}/${y}; fi
    echo ${y} -- ${trait}
    stata-mp -b do ${caprion}/utils/gwas2.do
  done
  for i in {0..3}
  do
    export y=${full[$i]}
    export trait=${abbrev[$i]}
    echo ${y} -- ${trait}
    head -1 ${caprion}/${y}/interval.*.All.txt
    grep -w rs113886122 ${caprion}/${y}/interval.*.All.txt
  done
# _invn
  export abbrev=(RCN3_44262548~n RCN3_44266666~R RCN3_All_invn RCN3_DR_invn)
  for i in {0..3}
  do
    export y=${full[$i]}_invn
    export trait=${abbrev[$i]}
    if [ ! -d ${caprion}/${y} ]; then mkdir ${caprion}/${y}; fi
    echo ${y} -- ${trait}
    stata-mp -b do ${caprion}/utils/gwas2_invn.do
  done

Note that long (full) names will be abbreviated (abbrev) by Stata, whose algorithm does not always produce unique names. We also have versions for raw data and inverse normalised (_invn) data.