From d6980082a05eb9a9e94473a19d99424b46ee3231 Mon Sep 17 00:00:00 2001 From: Zilong-Li Date: Wed, 21 Feb 2024 18:32:31 +0100 Subject: [PATCH] update readme and release v0.4.2 --- CHANGELOG.org | 3 ++- README.org | 11 +++++++---- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.org b/CHANGELOG.org index 45a5744..17643d1 100644 --- a/CHANGELOG.org +++ b/CHANGELOG.org @@ -1,6 +1,7 @@ - v0.4.2 - fix slowness due to the ld logics - + - add ld-clump functions + - v0.4.1 - fix ld windows - keep sites with higher maf in /prune.in/ diff --git a/README.org b/README.org index d20a046..55706a0 100644 --- a/README.org +++ b/README.org @@ -37,7 +37,7 @@ PCAone is a fast and memory efficient PCA tool implemented in C++ aiming at prov - [[#output-files][Output files]] - [[#running-mode][Running mode]] - [[#normalization][Normalization]] - - [[#ld-prune][LD prune]] + - [[#ld-pruning-and-clumping][LD pruning and clumping]] - [[#examples][Examples]] - [[#citation][Citation]] - [[#acknowledgements][Acknowledgements]] @@ -269,12 +269,15 @@ PCAone will automatically apply the standard normalization for genetic data. Add - 2: do count per median log transformation (usually for single cell RNA-seq data) One should choose proper normalization method for specific type of data. -** LD prune +** LD pruning and clumping -This is a novel LD prune method on admixed population. For more details, see our paper. +This is a novel statistics on LD calculation in admixed population. For more details, see our paper. #+begin_src shell -PCAone -b plink -k 3 -n 20 --svd 0 --ld-r2 0.8 --ld-window 1000000 --maf 0.05 +# pruning +PCAone -b plink -k 3 --ld-r2 0.8 --ld-bp 1000000 --maf 0.05 +# clumping +PCAone -b plink -k 3 --clump plink.assoc --clump-p1 0.0001 --clump-p2 0.01 --clump-r2 0.5 --maf 0.05 #+end_src ** Examples