From 6ac8222598b5366619158f5e6bbf592116c94e1a Mon Sep 17 00:00:00 2001
From: Thomas OBADIA <tobadia@pasteur.fr>
Date: Mon, 14 Feb 2022 14:52:18 +0100
Subject: [PATCH] Force reading Excel MFI input as text columns for to prevent
bugs with pivot_long() use mixing together sample/antigen names (character)
and MFI values (numbers).
---
FUNCTIONS.R | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/FUNCTIONS.R b/FUNCTIONS.R
index 95318d2..906d6a6 100644
--- a/FUNCTIONS.R
+++ b/FUNCTIONS.R
@@ -136,7 +136,7 @@ runRelativeAntibodyUnits = function(fname1, fname2, MFI_CSV, MFI_N_ANTIGENS, TEM
endcount_row_number <- which(L_full$xPONENT == "Avg Net MFI")
# Load Excel file
- L <- as.data.frame(read_excel(fname1, skip = median_row_number+1))
+ L <- as.data.frame(read_excel(fname1, skip = median_row_number+1, col_types = "text"))
## Find all blank rows (i.e. rows that are all NA).
## Then keep rows preceding the first blank row.
@@ -165,7 +165,7 @@ runRelativeAntibodyUnits = function(fname1, fname2, MFI_CSV, MFI_N_ANTIGENS, TEM
# MFI values as numeric
L[,-which(colnames(L) %in% c("Location","Sample","Total Events","TotalEvents"))] = lapply(L[,-which(colnames(L) %in% c("Location","Sample","Total Events"))], as.numeric)
- C <- as.data.frame(read_excel(fname1, skip = count_row_number+1))
+ C <- as.data.frame(read_excel(fname1, skip = count_row_number+1, col_types = "text"))
## Find all blank rows (i.e. rows that are all NA).
## Then keep rows preceding the first blank row.
--
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