Mercurial > repos > proteomisc > preprocess_dataset

comparison preprocess_datasets/Affymetrix_Preprocessing_Functions.R @ 15:4b3faf457c37 draft

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author proteomisc
date Sun, 03 Dec 2023 16:14:11 +0000
parents ebf6607b4e6a
children 471c893de71f
comparison
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14:0d544d449cca 15:4b3faf457c37
20 row.names=T, col.names=T,file="Matrix.Data.tsv") 20 row.names=T, col.names=T,file="Matrix.Data.tsv")
21 } 21 }
22 installed<-as.data.frame(installed.packages()) 22 installed<-as.data.frame(installed.packages())
23 lbraries=paste(annotation(data.sm),"db",sep='.') 23 lbraries=paste(annotation(data.sm),"db",sep='.')
24 if(!lbraries%in%installed$Package){ 24 if(!lbraries%in%installed$Package){
25 biocLite(lbraries[!lbraries%in%installed$Package])} 25 suppressWarnings(suppressMessages(require("BiocManager", quietly = TRUE)))
26 BiocManager::install(lbraries[!lbraries%in%installed$Package])}
26 27
27 suppressWarnings(suppressMessages(library(lbraries,character.only = TRUE))) 28 suppressWarnings(suppressMessages(library(lbraries,character.only = TRUE)))
28 29
29 symbol<-getSYMBOL(rownames(exprs(data.sm)), annotation(data.sm)) 30 symbol<-getSYMBOL(rownames(exprs(data.sm)), annotation(data.sm))
30 return(list(data.bg=data.bg,data.norm=data.norm,data.sm=data.sm,matrix_data=exprs(data.sm),symbol=symbol)) 31 return(list(data.bg=data.bg,data.norm=data.norm,data.sm=data.sm,matrix_data=exprs(data.sm),symbol=symbol))