External Validate

Example data

• DBSLMM result (your/path/out/summary_gemma_chr1.assoc.dbslmm.txt)
  The result of DBSLMM.
  
• External summary statistics (summary_external.txt)
  The summary statsitics of standing hright (GIANT data).
• Reference data (ref_chr1.bed, ref_chr1.bim and ref_chr1.fam)
  We sampled 300 samples from the 1000 Gemone Project data.
  Note: The phenotype of test data is simulated by normal distribution. Therefore, you can not use the test data to evaluate the prediction performance.

Input file format

• DBSLMM result
  

rs13302957 G 0.546652 1.82642 1
rs3748588 T 0.273432 1.64563 1
rs74045047 A -0.282306 -0.5378 1
rs3845292 G 0.159231 0.22554 1
rs113288277 T -0.0524222 -0.18273 1
rs112797925 A 0.252739 1.12303 1
rs12743678 A 0.741517 1.51564 1
rs141242758 C 0.00548007 0.0124342 0
rs28544273 A 0.0114189 0.0248473 0
rs3115860 C 0.00628248 0.013297 0

• External summary statistics
  

rs4747841 A 0.449 -0.000773760673593586
rs4749917 T 0.436 0.000771419263435909
rs878177 T 0.3 0.009073036977771
rs12219605 T 0.427 0.00076948282631908
rs3763688 C 0.144 -0.00109233489370248
rs3763689 T 0.217 -0.00466354028609167
rs1983867 C 0.431 0.00770375479879779
rs1983866 A 0.288 -0.0089655982510929
rs1983865 T 0.425 0.00769017229976026
rs1983864 T 0.3 -0.00907303697777101

• Reference panel (PLINK format)
  The same file name of bed, bim and fam files.

Input parameters

We prepare all the input file in the folder test_dat. You can output the explanation for each parameter:

Rscript VALID.R -h
Rscript VALID.R --help

The details is:

--dbslmm=CHARACTER
        INPUT:  the result of dbslmm
--external=CHARACTER
        INPUT:  the external summary statistics
--ref=CHARACTER
        INPUT:  the perfix of reference panel
--block=CHARACTER
        INPUT:  the block information (Berisa and Pickrell 2015)
--chr=CHARACTER
        INPUT:  the chromosome number
--mafMax=CHARACTER
        INPUT:  the maximium of the difference between reference panel and external data
--outPath=CHARACTER
        OUTPUT: the output path

Output

The output of VALID.R is the \(R^2\). It will be print in the screen.

Example code

We use the data of test_dat to show the external validation.

### change file permission 
valid=/your/path/DBSLMM/software/valid
chmod 777 ${valid}
### External validation
VALID=/your/path/DBSLMM/software/VALID.R
dbslmmRes=/your/path/DBSLMM/test_dat/out/summary_gemma_chr
summf=/your/path/DBSLMM/test_dat/external_summary
outPath=/your/path/DBSLMM/test_dat
ref=/your/path/DBSLMM/test_dat/ref_chr
blockf=/your/path/DBSLMM/test_dat/chr
### for chromosome 1 (example)
Rscript ${VALID} --dbslmm ${dbslmmRes} --external ${summf}.txt --ref ${ref} --valid ${valid} --block ${blockf} \
                 --chr 1 --mafMax 1 --outPath ${outPath}
### for whole genome (If you have whole genome data, you can use the command)
Rscript ${VALID} --dbslmm ${dbslmmRes} --external ${summf}.txt --ref ${ref} --valid ${valid} --block ${blockf} \
                 --chr all --mafMax 0.2 --outPath ${outPath}