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update readme
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Zilong-Li committed Dec 27, 2024
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Expand Up @@ -168,10 +168,7 @@ build PCAone from the source code, the following dependencies are required:
- GNU make
- zlib

We *recommend* building the software from source with MKL as backend to
maximize the performance. For MacOS users, we recommend using =llvm= by =brew
install llvm= instead of the default =clang= shipped with MacOS. Check out the
[[https://github.com/Zilong-Li/PCAone/blob/dev/.github/workflows/mac.yml#L21][mac workflow]].
We *recommend* building the software from source with MKL as backend to maximize the performance. For MacOS users, we recommend =llvm= by =brew install llvm= instead of the default =clang= shipped with MacOS. Check out the [[https://github.com/Zilong-Li/PCAone/blob/dev/.github/workflows/mac.yml#L21][mac workflow]].

*** With MKL or OpenBLAS as backend

Expand Down Expand Up @@ -296,14 +293,14 @@ This depends on your datasets, particularlly the relationship between number
of samples (=N=) and the number of variants / features (=M=) and the top PCs
(=k=). Here is an overview and the recommendation.

|--------------------------+-----------+----------------------|
| Method | Accuracy | Scenario |
|--------------------------+-----------+----------------------|
| IRAM (-d 0) | Very high | =N < 1000= |
| Window-Based RSVD (-d 2) | Very high | =M > 1,000,000= |
| RSVD (-d 1) | High | accuracy insensitive |
| Full SVD (-d 3) | Exact | cost insensitive |
|--------------------------+-----------+----------------------|
|--------------------------+-----------+-------------------------------------------|
| Method | Accuracy | Scenario |
|--------------------------+-----------+-------------------------------------------|
| IRAM (-d 0) | Very high | large scale data with =N < 5000= |
| Window-based RSVD (-d 2) | Very high | large scale data with =M > 1,000,000= |
| RSVD (-d 1) | High | accuracy insensitive, any scale data |
| Full SVD (-d 3) | Exact | cost insensitive, full variance explained |
|--------------------------+-----------+-------------------------------------------|

** Input formats

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