Commit cb3deb0578045972ebb5540d8827f7516f0b3c4d
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fc0d5afa8a
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Update that allows for more data set inputs at once
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55 additions
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RMatchGenes.R
| ... | ... | @@ -6,57 +6,64 @@ library(readr) |
| 6 | 6 | library(dplyr) |
| 7 | 7 | |
| 8 | 8 | Check2Match <- function(){ |
| 9 | -#Bring in the two files | |
| 10 | -##Number of rows with clinical data for first file | |
| 11 | -numrow1 <- "How many rows of clinical data are their in the first data set?: " %>% | |
| 9 | + numrows <- "How many rows of clinical data are their in the each data set?: " %>% | |
| 12 | 10 | readline(prompt = .) %>% |
| 11 | + strsplit(.,split = ",") %>% | |
| 12 | + .[[1]] %>% | |
| 13 | 13 | as.integer(.) |
| 14 | + i <- 1 | |
| 15 | + ANDIS <- select.list(choices = list.files(),multiple = TRUE, title = "Choose the file/files you want to analyze:") | |
| 14 | 16 | |
| 15 | -##Number of rows with clinical data for second file | |
| 16 | -numrow2 <- "How many rows of clinical data are their in the second data set?: " %>% | |
| 17 | - readline(prompt = .) %>% | |
| 18 | - as.integer(.) | |
| 19 | - | |
| 20 | -edfile <- file.choose() | |
| 21 | -ed <- edfile %>% | |
| 22 | - read_delim(.,delim = "\t") | |
| 23 | - | |
| 24 | -ednocd <- ed[-(1:numrow1),] | |
| 25 | -eddfile <- file.choose() | |
| 26 | -edd <- eddfile %>% | |
| 27 | - read_delim(.,delim = "\t") | |
| 17 | + for(i in 1:length(numrows)){ | |
| 18 | + if( i == 1){ | |
| 19 | + edfile <- ANDIS[i] | |
| 20 | + ed <- edfile %>% | |
| 21 | + read_delim(.,delim = "\t") | |
| 22 | + ednocd <- ed[-(1:numrows[1]),] | |
| 23 | + #Second file brought in | |
| 24 | + eddfile <- ANDIS[i + 1] | |
| 25 | + edd <- eddfile %>% | |
| 26 | + read_delim(.,delim = "\t") | |
| 27 | + eddnocd <- edd[-(1:numrows[2]),] | |
| 28 | + | |
| 29 | + ##Fully matched both data sets | |
| 30 | + eddy <- inner_join(ednocd,eddnocd) | |
| 31 | + #Matches | |
| 32 | + meds <- eddy[,1] | |
| 33 | + | |
| 34 | + } | |
| 35 | + if(i > 1 && i + 1 < length(numrows)){ | |
| 36 | + eddfile <- ANDIS[i + 1] | |
| 37 | + edd <- eddfile %>% | |
| 38 | + read_delim(.,delim = "\t") | |
| 39 | + eddnocd <- edd[-(1:numrows[i + 1]),] | |
| 40 | + ##Fully matched both data sets | |
| 41 | + eddy <- inner_join(meds,eddnocd) | |
| 42 | + meds <- eddy[,1] | |
| 28 | 43 | |
| 29 | -eddnocd <- edd[-(1:numrow2),] | |
| 30 | - | |
| 31 | -##Number of columns that belong to the first data file | |
| 32 | -numbcol1 <- dim(ednocd)[2] | |
| 33 | -##Number of columns that belong to the second data file | |
| 34 | -numbcol2 <- dim(eddnocd)[2] | |
| 35 | - | |
| 36 | -##Fully matched both data sets | |
| 37 | -eddy <- inner_join(ednocd,eddnocd) | |
| 38 | -#Matched ed | |
| 39 | -eddy[,1:numbcol1] | |
| 40 | -Finedm <- rbind(ed[1:numrow1,],eddy[,1:numbcol1]) | |
| 41 | -nam_fil_ed <- strsplit(edfile,"[\\|/]") %>% | |
| 42 | - .[[1]] %>% | |
| 43 | - .[length(.)] %>% | |
| 44 | - gsub("\\D","",.) %>% | |
| 45 | - c("GSE",.,"matched.txt") %>% | |
| 46 | - paste(collapse = "") | |
| 47 | -write.table(Finedm,file = nam_fil_ed,sep = "\t",row.names = FALSE) | |
| 48 | -#Matched edd | |
| 49 | -eddy[,(numbcol1 + 1):dim(eddy)[2]] | |
| 50 | -fineddm <- cbind(eddy[,1],eddy[,(numbcol1 + 1):dim(eddy)[2]]) | |
| 51 | -Fineddm <- rbind(edd[1:numrow2,],fineddm) | |
| 52 | -nam_fil_edd <- strsplit(eddfile,"[\\|/]") %>% | |
| 53 | - .[[1]] %>% | |
| 54 | - .[length(.)] %>% | |
| 55 | - gsub("\\D","",.) %>% | |
| 56 | - c("GSE",.,"matched.txt") %>% | |
| 57 | - paste(collapse = "") | |
| 58 | -write.table(Fineddm,file = nam_fil_edd,sep = "\t",row.names = FALSE) | |
| 59 | - | |
| 44 | + | |
| 45 | + } | |
| 46 | + i <- i + 1 | |
| 47 | + } | |
| 48 | + meds | |
| 49 | + for(j in 1:length(numrows)){ | |
| 50 | + edfile <- ANDIS[j] | |
| 51 | + ed <- edfile %>% | |
| 52 | + read_delim(.,delim = "\t") | |
| 53 | + ednocd <- ed[-(1:numrows[j]),] | |
| 54 | + #use meds to match | |
| 55 | + eddy <- inner_join(meds,ednocd) | |
| 56 | + Finedm <- rbind(ed[1:numrows[j],],eddy) | |
| 57 | + nam_fil_ed <- strsplit(edfile,"[\\|/]") %>% | |
| 58 | + .[[1]] %>% | |
| 59 | + .[length(.)] %>% | |
| 60 | + gsub("\\D","",.) %>% | |
| 61 | + c("GSE",.,"matched.txt") %>% | |
| 62 | + paste(collapse = "") | |
| 63 | + write.table(Finedm,file = nam_fil_ed,sep = "\t",row.names = FALSE) | |
| 64 | + j <- j + 1 | |
| 65 | + } | |
| 66 | + meds | |
| 60 | 67 | } |
| 61 | 68 | |
| 62 | 69 | -Check2Match() |
| 70 | +Check2Match() | |
| 63 | 71 | \ No newline at end of file |