A workflowr project.
The project folder is in the sumner /projects/compsci/vmp/USERS/heh/KOMP2022/.
raw data from LIMCS 2022-05-13.zip. I split the raw data into two zip files (2022-05-13-0.z01 and 2022-05-13-0.zip) less than 100mb using command:
zip 2022-05-13.zip --out 2022-05-13-0 -s 90m
use this command to unzip:
zip -F 2022-05-13-0.zip --out 2022-05-13.zip; unzip 2022-05-13.zip
Note: use the date name in the following Rscript for differentiating batches. for example here: batch = "2022-05-13"
If you run all the code in your local, please look over the parameter "projectDir and change it, in analysis/preprocessing_step1.R, analysis/preprocessing_step2.R and code/RCode_Functions_v3.R.
we are going to preprocess the raw data by running preprocessing_step1.R first and then running preprocessing_step2.R
cd /projects/compsci/vmp/USERS/heh/KOMP2022/analysis; nohup Rscript preprocessing_step1.R > preprocessing_step1.Rout 2>&1 &
cd /projects/compsci/vmp/USERS/heh/KOMP2022/analysis; nohup Rscript preprocessing_step2.R > preprocessing_step2.Rout 2>&1 &
Then open R file "analysis/run_AT_AllModels_script.R" and run it. it will generate the "analysis/run_AT_AllModels_script.sh" file.
Submit the job by the following command.
"cd /projects/compsci/vmp/USERS/heh/KOMP2022/analysis; chmod a+x run_AT_AllModels_script.sh; ./run_AT_AllModels_script.sh"
KOMP_AT.Rmd will generate all the figures for the association results.