From 5aa541e26c46fccc4e3ffe2e3766d50d49086abe Mon Sep 17 00:00:00 2001 From: roddypr Date: Mon, 6 Dec 2021 12:59:54 +0000 Subject: [PATCH] minor corrections --- .../Polymorphisms in invicta and richteri/README.md | 2 ++ .../shared_private.rmd | 8 -------- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/Private and shared alleles/Polymorphisms in invicta and richteri/README.md b/Private and shared alleles/Polymorphisms in invicta and richteri/README.md index e09d6f9..b64dc7d 100644 --- a/Private and shared alleles/Polymorphisms in invicta and richteri/README.md +++ b/Private and shared alleles/Polymorphisms in invicta and richteri/README.md @@ -148,6 +148,8 @@ wc -l results/snp_frequencies.csv grep -c supergene results/snp_frequencies.csv # 39210 +rm -rf results/by_scaff + ``` diff --git a/Private and shared alleles/Polymorphisms in invicta and richteri/shared_private.rmd b/Private and shared alleles/Polymorphisms in invicta and richteri/shared_private.rmd index 2145e65..c34e779 100644 --- a/Private and shared alleles/Polymorphisms in invicta and richteri/shared_private.rmd +++ b/Private and shared alleles/Polymorphisms in invicta and richteri/shared_private.rmd @@ -191,14 +191,6 @@ private_alleles <- function(freq_matrix, pop) { } -private_to_invicta_bb <- private_alleles(allele_frequencies_ma, pop="invicta_bb") -private_to_richteri_bb <- private_alleles(allele_frequencies_ma, pop="richteri_bb") - -allele_frequencies_ma <- snp_freq[, c("daf_invicta_bb", "daf_invicta_lb", "daf_richteri_bb", "daf_richteri_lb")] -allele_frequencies_ma <- as.matrix(allele_frequencies_ma) - - - snp_freq$private_to_richteri <- snp_freq$daf_invicta_bb == 0 & snp_freq$daf_invicta_lb == 0 & (snp_freq$daf_richteri_bb > 0 | snp_freq$daf_richteri_lb > 0 )