Hello,
I am currently trying to perform PRSice-2 on OCD data. My base data is GWAS conducted on OCD and my target data only included OCD-confirmed people. However, I keep receiving the following issue where execution is halted and I do not receive PRS scores: "There are no control samples". How should I go about this?
The log file is featured below and thank you so much for your help!
Sincerely,
-S
If you use PRSice in any published work, please cite:
Choi SW, O'Reilly PF.
PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data.
GigaScience 8, no. 7 (July 1, 2019)
2022-12-14 13:24:19
./PRSice_linux \
--a1 A1 \
--a2 A2 \
--bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \
--base ocd_aug2017 \
--base-info INFO:0.9 \
--binary-target T \
--bp BP \
--chr CHR \
--clump-kb 250kb \
--clump-p 1.000000 \
--clump-r2 0.100000 \
--cov OCD.cov \
--interval 5e-05 \
--lower 5e-08 \
--num-auto 22 \
--out PRSice \
--pheno OCD.status \
--pvalue P \
--seed 2085699930 \
--snp SNP \
--stat BETA \
--target ocd_ts_final \
--thread 1 \
--upper 0.5
Base file: ocd_aug2017
Header of file is:
CHR SNP BP A1 A2 INFO OR SE P
Reading 100.00%
8409516 variant(s) observed in base file, with:
2041240 variant(s) with INFO score less than 0.900000
978270 ambiguous variant(s) excluded
5390006 total variant(s) included from base file
Loading Genotype info from target
==================================================
73 people (0 male(s), 0 female(s)) observed
73 founder(s) included
Warning: Currently not support haploid chromosome and sex
chromosomes
93903 variant(s) not found in previous data
84 variant(s) with mismatch information
556143 variant(s) included
Phenotype file: OCD.status
Column Name of Sample ID: FID+IID
Note: If the phenotype file does not contain a header, the
column name will be displayed as the Sample ID which is
expected.
There are a total of 1 phenotype to process
Start performing clumping
Clumping Progress: 100.00%
Number of variant(s) after clumping : 85037
Processing the 1 th phenotype
Phenotype is a binary phenotype
0 control(s)
73 case(s)
There are no control samples
Error:
Execution halted
Hello, I am currently trying to perform PRSice-2 on OCD data. My base data is GWAS conducted on OCD and my target data only included OCD-confirmed people. However, I keep receiving the following issue where execution is halted and I do not receive PRS scores: "There are no control samples". How should I go about this?
The log file is featured below and thank you so much for your help! Sincerely, -S
If you use PRSice in any published work, please cite: Choi SW, O'Reilly PF. PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data. GigaScience 8, no. 7 (July 1, 2019) 2022-12-14 13:24:19 ./PRSice_linux \ --a1 A1 \ --a2 A2 \ --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \ --base ocd_aug2017 \ --base-info INFO:0.9 \ --binary-target T \ --bp BP \ --chr CHR \ --clump-kb 250kb \ --clump-p 1.000000 \ --clump-r2 0.100000 \ --cov OCD.cov \ --interval 5e-05 \ --lower 5e-08 \ --num-auto 22 \ --out PRSice \ --pheno OCD.status \ --pvalue P \ --seed 2085699930 \ --snp SNP \ --stat BETA \ --target ocd_ts_final \ --thread 1 \ --upper 0.5
Initializing Genotype file: ocd_ts_final (bed)
Start processing ocd_aug2017 ==================================================
Base file: ocd_aug2017 Header of file is: CHR SNP BP A1 A2 INFO OR SE P
Reading 100.00% 8409516 variant(s) observed in base file, with: 2041240 variant(s) with INFO score less than 0.900000 978270 ambiguous variant(s) excluded 5390006 total variant(s) included from base file
Loading Genotype info from target ==================================================
73 people (0 male(s), 0 female(s)) observed 73 founder(s) included
Warning: Currently not support haploid chromosome and sex chromosomes
93903 variant(s) not found in previous data 84 variant(s) with mismatch information 556143 variant(s) included Phenotype file: OCD.status Column Name of Sample ID: FID+IID Note: If the phenotype file does not contain a header, the column name will be displayed as the Sample ID which is expected. There are a total of 1 phenotype to process Start performing clumping Clumping Progress: 100.00% Number of variant(s) after clumping : 85037 Processing the 1 th phenotype Phenotype is a binary phenotype 0 control(s) 73 case(s) There are no control samples Error: Execution halted