From now on, I will try to archive our update log here.
- Thanks to report from @charlisech, we were able to pinpoint a bug related to sample selection when using bgen data.
- Fix off by one error in PRSet best score output
- Fix problem for bgen file when sample selection is performed on bgen files containing sample information
- Fix bug where SNPs without missingness will be wrongly considered as having 100% missingness
- Fix error log where PRSice should now correct stat if a parameter is missing the required arguments
- Fix segmentation fault when
- Fix problem with missing covariate
- Fix Rscript such that it properly read in phenotype file when
--pheno-co lis specified
- Fix best score output when
- Also fix Rscript covariate and phenotype file read when handling IDs star
t with 00 and when
- Fix bar plot with covariate. Was plotting the full R2 instead of the PRS.R2
- Update Rscript such that it match features in executable (thus avoid problem in plotting)
- Fix a bug where PRSice will crash when there are missing covariates
- Fix Rscript bar plot problem
- Fix problem introduced by previous fix.
- Was hoping 2.3.0's unit test will help reducing the amount of bugs. Sorry for the troubles.
- Fix all score output format
- Fix problem with
--no-regress. Might still have problem with
--no-regress --score con-std
- Fix error where sample selection will distort phenotype loading, loading the wrong phenotype to wrong sample. As this is a major bug, we deleted the previous 2 releases. Sorry for the troubles.
- Fix output error where we always say 0 valid phenotype were included for continuous trait
- Fix problem with permutation where PRSice will crash if input are rank deficient
- Fix problem when provide a binary phenotype file with a fam file containing -9 as phenotype, PRSice will wrongly state that there are no phenotype presented
- Fix problem in Rscript where if sample ID is numeric and starts with 0, the best file will not merge with the phenotype file, causing 0 valid PRS to be observed
- We now support multi-threaded clumping (separated by chromosome)
- Genotypes will be stored to memory during clumping (increase memory usage, significantly speed up clumping)
- Will only generate one .prsice file for all phenotypes
- .prsice file now has additional column call "Pheno"
--chr-idwhich generate rs id based on user provided formula (see detail for more info)
- Format of
--base-infoare now changed to
- Fix a bug related to ambiguous allele dosage flipping when
- Better mismatch handling. For example, if your base file only provide the effective allele A without the non-effective allele information, PRSice will now do dosage flipping if your target file has G/C as effective allele and A /T as an non-effective allele (whereas previous this SNP will be considered as a mismatch)
- Fix bug in 2.2.13 where PRSice won't output the error message during command parsing stage
- If user provided the
--statinformation, PRSice will now error out instead of trying to look for BETA or OR in the file.
- PRSice should now better recognize if phenotype file contains a header
- various small bug fix