Mercurial > repos > proteomisc > preprocess_dataset
comparison preprocess_datasets/Make_matrix_two_channels.R @ 27:b5eac045873c draft
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| author | proteomisc |
|---|---|
| date | Mon, 04 Dec 2023 12:41:06 +0000 |
| parents | ebf6607b4e6a |
| children |
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| 26:a085ddc4cb46 | 27:b5eac045873c |
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| 1 make_design<-function(MA_matrix){ | |
| 2 matrix<-RG.MA(MA_matrix$dataNBA) | |
| 3 colnames_matrix<-NULL | |
| 4 tmp<-strsplit(colnames(MA_matrix$dataNBA),split=".",fixed = T) | |
| 5 for(i in 1:ncol(MA_matrix$dataNBA)){ | |
| 6 colnames_matrix[i]<-paste(tmp[[i]][1],"R",sep=".") | |
| 7 | |
| 8 # .Red intensity | |
| 9 } | |
| 10 i=1; | |
| 11 for(j in (ncol(MA_matrix$dataNBA)+1):((ncol(MA_matrix$dataNBA)*2))){ | |
| 12 | |
| 13 colnames_matrix[j]<-paste(tmp[[i]][1],"G",sep=".") | |
| 14 i<-i+1; | |
| 15 # .Green intensity | |
| 16 } | |
| 17 matrix_data<-cbind(matrix$R,matrix$G) | |
| 18 colnames(matrix_data)<-colnames_matrix | |
| 19 rownames(matrix_data)<-rownames(MA_matrix$dataNBA) | |
| 20 MA_matrix$matrix_data<-log2(matrix_data) | |
| 21 groupe<-c(rep("case",ncol(matrix$R)),rep("control",ncol(matrix$G))) | |
| 22 sample=colnames(matrix_data) | |
| 23 designo<-data.frame(sample=sample,groupetype=rep(designo$group,2),group=groupe) | |
| 24 MA_matrix$designo<-designo | |
| 25 write.table(format(designo, justify="right"),sep="\t", quote=FALSE, | |
| 26 row.names=T, col.names=T,file="design.txt") | |
| 27 return(MA_matrix) | |
| 28 } |