tidyup

README.org

@@ -2,7 +2,7 @@
 #+subtitle: Version 0.4.7 
 #+author: Zilong Li 
 #+email: [email protected]
-#+options: toc:2 num:t email:t
+#+options: toc:2 num:nil email:t
 #+latex_compiler: xelatex
 #+latex_class: article
 #+latex_class_options: [a4paper, 11pt]
@@ -15,8 +15,6 @@
 #+latex_header: \hypersetup{colorlinks=true, linkcolor=blue}
 #+latex: \clearpage
 
-* Bad :noexport:
-
 [[https://github.com/Zilong-Li/PCAone/actions/workflows/linux.yml/badge.svg]]
 [[https://github.com/Zilong-Li/PCAone/actions/workflows/mac.yml/badge.svg]]
 [[https://bioconda.github.io/recipes/pcaone/README.html][https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat]]
@@ -462,6 +460,12 @@ Currently, the LD R2 for pairwise SNPs within a window can be outputted via =--p
          -o adj
 #+end_src
 
+We provide the
+[[https://github.com/Zilong-Li/PCAone/blob/main/scripts/calc_decay_bin.R][calc_decay_bin.R]]
+script to parse the output file =.ld.gz= and calculate the average R2 for each
+bin as well as plotting. We also provide the nextflow
+[[https://github.com/Zilong-Li/PCAone/blob/main/workflows/ld.nf][ld.nf]] for
+benchmarking the LD statistics.
 
 ** Prunning based on Ancestry-Adjusted LD
 

scripts/calc_decay_bin.R

@@ -46,5 +46,5 @@ res <- do.call(rbind.data.frame, res)
 res$bin <- res$bin * (window / nbins)
 colnames(res) <- c("chr", "distance", "num", "avg_R2", "std")
 
-write.table(res, fout, sep = "\t", col.names = F, row.names = F, quote = F)
+write.table(res, fout, sep = "\t", row.names = F, quote = F)