Jingan Qu / r_code

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Commit 658ed0df54291b9bdcc2ac2ed94a29e598a022a1

Authored by Jingan Qu
1 parent b688af3fe9
Exists in master

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Showing 2 changed files with 820 additions and 13 deletions   Show diff stats
... ... @@ -0,0 +1,791 @@
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... ... @@ -2,7 +2,7 @@
2 2  
3 3 #set the working directory
4 4 #make it be the data file
5   -setwd("/Users/jinganqu/Dropbox/Research/Biostat/data_cleaning/data")
  5 +setwd("/home/qja0428/Dropbox/research/Biostat/data")
6 6  
7 7  
8 8 datafiles <- list.files()
... ... @@ -35,12 +35,18 @@ for (i in seq_along(datafiles)){
35 35 #find how many the platform_id
36 36 platID <- grep("Sample_platform_id", dataset[,1],fixed = TRUE)
37 37  
  38 + name <- c("sampleID","platform","gender","age")
38 39  
  40 + #store all the information
  41 + infor <- data.frame(name)
  42 +
  43 + #store all the data we need
  44 + gene <- data.frame()
39 45  
40 46 for (j in seq_along(sampleID)) {
41 47 #get the data
42 48 tmp_data <- dataset[(begin[j]+2):(end[j]-1),1:2]
43   - tmp_data[,2] <- as.numeric(tmp_data[,2])
  49 + tmp_data[,2] <- tmp_data[,2]
44 50  
45 51 #get the exact information
46 52 #get the sample#
... ... @@ -54,16 +60,32 @@ for (i in seq_along(datafiles)){
54 60 Age <- strsplit(dataset[age[j],1], ": ")[[1]][2]
55 61 Age <- as.numeric(Age)
56 62  
  63 + #store the information into the data frame
  64 + infor <- cbind(infor, c(sam, platform, gender, Age))
  65 +
57 66 #combine the data into temple data
58   - n <- nrow(tmp_data)
59   - tmp_data <- cbind(tmp_data, rep(sam,n), rep(platform,n),
60   - rep(gender, n), rep(Age, n))
  67 + if (j == 1){
  68 + gene <- tmp_data
  69 + } else {
  70 + gene <- cbind(gene, tmp_data[,2])
  71 + }
  72 +
  73 +
  74 +
61 75  
62   - #combine the temple data into output
63   - output <- rbind(output, tmp_data)
64 76  
65 77 }
66 78  
  79 + #output the result we get
  80 + names(infor) <- ""
  81 + names(gene) <- ""
  82 + output <- rbind(infor, gene)
  83 +
  84 + file_name <- paste0(platform,".csv")
  85 + location <- file.path("/home/qja0428/Dropbox/research/Biostat",file_name)
  86 +
  87 + write.csv(output,location, row.names = FALSE)
  88 +
67 89  
68 90 #check how many the platform_id
69 91 # platform <- dataset[platID, 1]
... ... @@ -84,12 +106,6 @@ for (i in seq_along(datafiles)){
84 106  
85 107 }
86 108  
87   -#name the columns
88   -names(output) <- c("ID_REF","Value","Sample","Platform","Gender","Age")
89   -
90   -#save the output into local
91   -setwd("/Users/jinganqu/Dropbox/Research/Biostat/data_cleaning")
92   -write.csv(output, "output.csv", row.names = F)
93 109  
94 110  
95 111