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Fix arguments in value_transformation #24

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merged 1 commit into from
Nov 25, 2021
Merged

Fix arguments in value_transformation #24

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8 changes: 4 additions & 4 deletions transcriptomic_data/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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`:
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6 changes: 3 additions & 3 deletions transcriptomic_data/value_transformation.R
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@@ -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)){
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