From now on, I will try to archive our update log here.
2020-08-05 (v2.3.3)
- Thanks to report from @charlisech, we were able to pinpoint a bug related to sample selection when using bgen data.
2020-07-15 (v2.3.2)
- 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
2020-05-30 (v2.3.1.e)
- 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
2020-05-29 (v2.3.1.d)
- Fix segmentation fault when
--ld
is used
2020-05-28 (v2.3.1.c)
- Fix problem with missing covariate
- Fix Rscript such that it properly read in phenotype file when
--pheno-co l
is specified
2020-05-26 (v2.3.1.b)
- Fix best score output when
--ignore-fid
is used - Also fix Rscript covariate and phenotype file read when handling IDs star
t with 00 and when
--ignore-fid
is used
2020-05-26 (v2.3.1.a)
- Fix bar plot with covariate. Was plotting the full R2 instead of the PRS.R2
2020-05-23 (v2.3.1)
- 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
2020-05-21 (v2.3.0.e)
- Fix Rscript bar plot problem
2020-05-21 (v2.3.0.d)
- 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.
2020-05-20 (v2.3.0.c)
- Fix all score output format
- Fix problem with
--no-regress
. Might still have problem with--no-regress --score con-std
2020-05-19 (v2.3.0.b)
- 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.
2020-05-19 (v2.3.0.a)
- 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
2020-05-18 (v2.3.0)
- 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"
- Introduced
--chr-id
which generate rs id based on user provided formula (see detail for more info) - Format of
--base-maf
and--base-info
are now changed to<name>:<value>
from<name>,<value>
- Fix a bug related to ambiguous allele dosage flipping when
--keep-ambig
is used - 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
--stat
information, 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