Mercurial > repos > sarahinraauzeville > tax4fun
comparison sm_Tax4Fun.R @ 10:444f1e7fe177 draft
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| author | sarahinraauzeville |
|---|---|
| date | Thu, 21 Dec 2017 09:09:09 -0500 |
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| 9:bd5ba02b1f71 | 10:444f1e7fe177 |
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| 1 # The function ------------------------------------- | |
| 2 #--------------------------------------------------- | |
| 3 GalaxyFrogsTax <- function(input.file, | |
| 4 reference, | |
| 5 output.file = "Tax4FunProfile.txt" | |
| 6 ) { | |
| 7 library(Tax4Fun) | |
| 8 folderReferenceData<- reference | |
| 9 | |
| 10 Tax4FunOutput<-Tax4Fun(importSilvaNgsData(input.file), folderReferenceData) # optionnal: fctProfiling = TRUE, refProfile = "UProc", shortReadMode = TRUE, normCopyNo = TRUE) | |
| 11 #folderReferenceData (required): a character vector with one character string indicating the folder location of the unzipped reference data. The reference data can be obtained from the Tax4Fun website http://tax4fun.gobics.de/ ("SILVA Reference data"). | |
| 12 #reference = "/galaxydata/galaxy-preprod/my_tools/sm_Tax4Fun/SILVA123/" | |
| 13 | |
| 14 Tax4FunProfile <- Tax4FunOutput$Tax4FunProfile | |
| 15 Tax4FunProfile <- data.frame(t(Tax4FunOutput$Tax4FunProfile)) | |
| 16 #View(Tax4FunProfile) | |
| 17 | |
| 18 write.table(Tax4FunProfile, "Tax4FunProfile.txt", sep="\t") | |
| 19 | |
| 20 } #fin de la fonction |