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| author | Alexander Kabui | 2021-10-13 14:36:34 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2022-01-22 09:23:14 +0300 |
| commit | 8981ef0585dd6b74b6719faa886d0c9880f18698 (patch) | |
| tree | 58a64e5adbe9a74e84deb84395620e1535e518cc | |
| parent | fa4bc9a68b37bceaaacf6d00e69413ba829b3e77 (diff) | |
| download | genenetwork3-8981ef0585dd6b74b6719faa886d0c9880f18698.tar.gz | |
get significant interactions
| -rw-r--r-- | scripts/ctl_analysis.R | 5 |
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) |