Commit 131711985086e2a5856937a57f7d4ea89de4f22c
1 parent
e53c3c5908
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master
An automated version of RCleanDscret.R
Working on outputting more insightful errors and warnings. (UNTESTED)
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RAutoClDs.R
| ... | ... | @@ -14,45 +14,45 @@ library(stringr) |
| 14 | 14 | chngrownm <- function(mat){ |
| 15 | 15 | row <- dim(mat)[1] |
| 16 | 16 | col <- dim(mat)[2] |
| 17 | - j <- 1 | |
| 18 | - x <- 1 | |
| 19 | - p <- 1 | |
| 20 | - a <- 1 | |
| 21 | - b <- 1 | |
| 17 | + e <- 1 | |
| 18 | + r <- 1 | |
| 19 | + a <- 1 | |
| 20 | + h <- 1 | |
| 22 | 21 | g <- 1 |
| 23 | - for(j in 1:col){ | |
| 24 | - if("!Sample_source_name_ch1"==mat[1,j]){ | |
| 25 | - colnames(mat)[j] <- "Brain_Region" | |
| 22 | + o <- 1 | |
| 23 | + for(e in 1:col){ | |
| 24 | + if("!Sample_source_name_ch1"==mat[1,e]){ | |
| 25 | + colnames(mat)[e] <- "Brain_Region" | |
| 26 | 26 | } |
| 27 | - if("!Sample_title" == mat[1,j]){ | |
| 28 | - colnames(mat)[j] <- "Title" | |
| 27 | + if("!Sample_title" == mat[1,e]){ | |
| 28 | + colnames(mat)[e] <- "Title" | |
| 29 | 29 | } |
| 30 | - if("!Sample_geo_accession" == mat[1,j]){ | |
| 31 | - colnames(mat)[j] <- "ID_REF" | |
| 30 | + if("!Sample_geo_accession" == mat[1,e]){ | |
| 31 | + colnames(mat)[e] <- "ID_REF" | |
| 32 | 32 | } else{ |
| 33 | - if(grepl("Sex|gender|Gender|sex",mat[2,j])==TRUE){ | |
| 34 | - colnames(mat)[j] <- paste0("Sex",x) | |
| 35 | - x = x + 1 | |
| 33 | + if(grepl("Sex|gender|Gender|sex",mat[2,e])==TRUE){ | |
| 34 | + colnames(mat)[e] <- paste0("Sex",r) | |
| 35 | + r = r + 1 | |
| 36 | 36 | } |
| 37 | - if(grepl("postmorteminterval|PMI|pmi",mat[2,j])==TRUE){ | |
| 38 | - colnames(mat)[j] <- paste0("PMI",p) | |
| 39 | - p = p + 1 | |
| 40 | - } | |
| 41 | - if(grepl("age|Age|AGE",mat[2,j])==TRUE){ | |
| 42 | - colnames(mat)[j] <- paste0("Age",a) | |
| 37 | + if(grepl("postmorteminterval|PMI|pmi",mat[2,e])==TRUE){ | |
| 38 | + colnames(mat)[e] <- paste0("PMI",a) | |
| 43 | 39 | a = a + 1 |
| 44 | - } | |
| 45 | - if(grepl("braak|b&b",mat[2,j])==TRUE){ | |
| 46 | - colnames(mat)[j] <- paste0("Braak",b) | |
| 47 | - b = b + 1 | |
| 48 | 40 | } |
| 49 | - if(grepl("group|disease|control|AD|normal|diagnosis|Alzheimer|Control|Normal",mat[2,j])==TRUE){ | |
| 50 | - colnames(mat)[j] <- paste0("Group",g) | |
| 41 | + if(grepl("age|Age|AGE",mat[2,e])==TRUE){ | |
| 42 | + colnames(mat)[e] <- paste0("Age",h) | |
| 43 | + h = h + 1 | |
| 44 | + } | |
| 45 | + if(grepl("braak|b&b",mat[2,e])==TRUE){ | |
| 46 | + colnames(mat)[e] <- paste0("Braak",g) | |
| 51 | 47 | g = g + 1 |
| 52 | 48 | } |
| 49 | + if(grepl("group|disease|control|AD|normal|diagnosis|Alzheimer|Control|Normal",mat[2,e])==TRUE){ | |
| 50 | + colnames(mat)[e] <- paste0("Group",o) | |
| 51 | + o = o + 1 | |
| 52 | + } | |
| 53 | 53 | |
| 54 | 54 | } |
| 55 | - j = j + 1 | |
| 55 | + e = e + 1 | |
| 56 | 56 | } |
| 57 | 57 | mat |
| 58 | 58 | } |