Version History¶

0.11

Fix the bug for OLS to compute adjusted r squared.

0.13

Add --keep command to enable user to specify a file that contains the subjects ID SuShiE will perform on. Add --ancestry_index command to enable user to specify a file that contains the ancestry index for fine-mapping. With this, user can input single phenotype, genotype, and covariate file that contains all the subjects across ancestries. Implement padding to increase inference time. Record elbo at each iteration and can access it in the infer.SuShiEResult object. The alphas table now outputs the average purity and KL divergence for each L. Change --kl_threshold to --divergence. Add --maf command to remove SNPs that less than minor allele frequency threshold within each ancestry. Add --max_select command to randomly select maximum number of SNPs to compute purity to avoid unnecessary memory spending. Add a QC function to remove duplicated SNPs.

0.15

Fix several typos; add a sanity check on reading vcf genotype data by assigning gt_types==Unknown as NA; Add preprint information. |

0.17

Fix several bugs, add debug checkpoints, add chrom, start, and end filtering to individual-level fine-mapping, enhance codes quality, and update readme for official publication.