From 83cdc3c97e02af2fec4c3f9f9003ddd8e833fd5f Mon Sep 17 00:00:00 2001
From: "Vera N. Karlbauer" <vera@karlbauer.org>
Date: Fri, 7 Mar 2025 11:12:56 +0100
Subject: [PATCH] Only include IDs where sex could be predicted

---
 scripts/4_check_matching_of_epigenetic_sex.Rmd | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/4_check_matching_of_epigenetic_sex.Rmd b/scripts/4_check_matching_of_epigenetic_sex.Rmd
index 736dafd..bf8ac07 100644
--- a/scripts/4_check_matching_of_epigenetic_sex.Rmd
+++ b/scripts/4_check_matching_of_epigenetic_sex.Rmd
@@ -54,6 +54,7 @@ fail the sex match check
 
 ```{r, predict sex with DNAm data, include= FALSE}
 predictedSex <- getSex(gRatioSet_quality, cutoff=-2)
+phenotype_data <- subset(phenotype_data, arrayid %in% rownames(predictedSex),)
 
 sex_df <- phenotype_data %>%
   select(personid, arrayid, reported_sex = sex) %>%