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authorAlexander Kabui2021-10-13 14:36:34 +0300
committerBonfaceKilz2022-01-22 09:23:14 +0300
commit8981ef0585dd6b74b6719faa886d0c9880f18698 (patch)
tree58a64e5adbe9a74e84deb84395620e1535e518cc /scripts
parentfa4bc9a68b37bceaaacf6d00e69413ba829b3e77 (diff)
downloadgenenetwork3-8981ef0585dd6b74b6719faa886d0c9880f18698.tar.gz
get significant interactions
Diffstat (limited to 'scripts')
-rw-r--r--scripts/ctl_analysis.R5
1 files changed, 4 insertions, 1 deletions
diff --git a/scripts/ctl_analysis.R b/scripts/ctl_analysis.R
index 04b55f9..6c3b22f 100644
--- a/scripts/ctl_analysis.R
+++ b/scripts/ctl_analysis.R
@@ -1,6 +1,8 @@
library(ctl)
# The genotypes.csv file containing the genotype matrix is stored individuals (rows) x genetic marker (columns):
+
+
genotypes <- read.csv("genotypes.csv",row.names=1, header=FALSE, sep="\t")
# The phenotypes.csv file containing individuals (rows) x traits (columns) measurements:
traits <- read.csv("phenotypes.csv",row.names=1, header=FALSE, sep="\t")
@@ -11,6 +13,7 @@ ctls <- CTLscan(geno,traits,strategy=input$strategy,
nthreads=6,verbose=TRUE)
-# plots and ctl networks
+#output matrix significant CTL interactions with 4 columns: trait, marker, trait, lod
+sign <- CTLsignificant(ctls,significance = input$significance)