When we implement PRSice 2, there are some concious choice we have made. Here are some of the decisions we have made during the implementation of PRSice
Support of BGEN v1.3¶
While it is straightforward to support BGEN v1.3 as we are using the bgen library directly, we have purposefully disabled its support to avoid the inclusion of the zstd library. This is because - UKBB is v1.2 - We are not familiar with the licensing of zstd library
Removal of PCA calculation¶
The main goal of PRSice 2 is to support the polygenic score analysis on large scale data. With such data, the calculation of PCA on the fly will be time consuming and will require specific algorithms such as those implemented in flashPCA. In order to support the in-place PCA calculation, not only will we have to implement the flashPCA algorithm, we will also need to implement prunning, which is required prior to PCA calculation.
Due to the lack of man power, we therefore decided that we will not implement the PCA calculation. Another reasoning is that we believe users should first examine the PCA results before directly applying them to the PRS analysis.