Merge pull request #24 from pasmopy/value-transformation

Fix arguments in `value_transformation`
pasmopy · Nov 25, 2021 · 7500183 · 7500183
2 parents bfff564 + d33a43e
commit 7500183
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diff --git a/transcriptomic_data/README.md b/transcriptomic_data/README.md
@@ -130,19 +130,19 @@ COAD_TPM <- fread("TPM_RLE_postComBat_COAD_BREAST.csv")
 gene <- scan(gene.txt, what="character")
 cellline <- c("MCF7_BREAST", "BT474_BREAST", "SKBR3_BREAST", "MDAMB231_BREAST")
 
-value_transformation(upstream = BRCA_TPM,
-                     origin = COAD_TPM,
+value_transformation(origin = BRCA_TPM,
+                     upstream = COAD_TPM,
                      gene = gene,
                      cellline = cellline,
                      outputfile = "TPM_RLE_postComBat_COAD_BREAST.csv")
 ```
 
 **Parameters**:
 
-- `upstream`:  
+- `origin`:  
   Gene expression data used for parameter estimation.
 
-- `origin`:  
+- `upstream`:  
   Gene expression data for the samples for which you want to predict dynamics using the parameters estimated by `optimizeddata`.
 
 - `gene`:  

diff --git a/transcriptomic_data/value_transformation.R b/transcriptomic_data/value_transformation.R
@@ -1,9 +1,9 @@
 
 #value_transformation
 
-value_transformation <- function(upstream, origin, gene, cellline, outputfile){
-  optimizeddata_genelist <- upstream[upstream$Description %in% genelist,]
-  newdata_genelist <- origin[origin$Description %in% genelist,]
+value_transformation <- function(origin, upstream, gene, cellline, outputfile){
+  optimizeddata_genelist <- origin[origin$Description %in% genelist,]
+  newdata_genelist <- upstream[upstream$Description %in% genelist,]
 
   newdata_converted <- c()
   for(i in 1:length(gene)){