Note: run org.genvisis.cnv.gwas.utils.GeneScorePipeline -h
to see what is required to run the pipeline.
Create files:
Genetic dataset
data.txt file that points to genetic dataset (tab-delimited file – D
Effect files saved as .meta files
.pheno files
Create a location directory for GSP (e.g., GSP)
Run GSP from the directory above the GSP directory.
To run interactively:
module load R/3.5.0
jcp org.genvisis.cnv.gwas.utils.GeneScorePipeline workDir=/ rLibsDir=/
To submit as job (.qsub) saved above GSP directory:
echo "start GSP at: " date
cd DIRECTORYNAME
module load R/3.5.0
java -Djava.awt.headless=true -Xmx16G -jar plab-internal.jar org.genvisis.cnv.gwas.utils.GeneScorePipeline workDir=./GSP rLibsDir=
echo "end GSP at: " date
Result Column | Explanation |
---|---|
STUDY | study name |
DATAFILE | Data file used for results line |
INDEX-THRESHOLD | |
FACTOR | .pheno filename used for results line |
BASE-R-SQUARED | r2 for model ran using genetics only no covariates |
R-SQR | r2 for model ran using genetics with covariates |
R-DIFF | difference between the two r2; larger is better |
P-VALUE | from software |
EXCEL-SIG | p-value calculated in excel |
BETA | effect estimate for the risk score |
SE | standard error of the effect estimate |
NUM | total number used in analysis |
CASES | total number of cases used in the analysis (if continuous pheno will be NA) |
CONTROLS | total number of controls used in the analysis (if continuous pheno will be NA) |
PAIRED-T-P-VALUE | used with TRIOS; average of parent compared to child (N/A if not a trio) |
WILCOXON-SIGNED-RANK-P-VALUE | used with TRIOS; average of parent compared to child (N/A if not a trio) |
PAIRED-STAT-NUM-TRIOS | used with TRIOS; average of parent compared to child (0 if not a trio) |
#sigInMeta | <5x10-08 (number of variants in the metafile that were below the 5x10^-8 threshold [or whatever threshold you specified in the command]) |
#indexVariantsInMeta | Number we have in our dataset |
#indexVariantsInDataset | Number we have in our dataset |
B-F-SCORE | How much is captured if T < U : missingness; ideal =1 |
INVCHI-SCORE | How much is captured if T < U : missingness; ideal =1 |
Column names can be any from a list of allowed aliases, e.g., ‘SNP’ instead of ‘MarkerName’. Column aliases are defined in the Genvisis source code in the org.pankratzlab.common.Aliases class, using: MARKER_NAMES CHRS POSITIONS EFFECTS ALLELE_FREQS PVALUES STD_ERRS