Commit 498d25a3e5245d2cbaa767c0d74807a65fd4c521
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2bf073a859
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For matching genes between two consolidated data files (UNTESTED)
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RMatchGenes.R
| File was created | 1 | #Checking for similar genes in both data sets | |
| 2 | |||
| 3 | #Required libraries | ||
| 4 | library(MASS) | ||
| 5 | library(readr) | ||
| 6 | library(dplyr) | ||
| 7 | |||
| 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?: " %>% | ||
| 12 | readline(prompt = .) %>% | ||
| 13 | as.integer(.) | ||
| 14 | |||
| 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") | ||
| 28 | |||
| 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 | |||
| 60 | } | ||
| 61 | |||
| 62 | Check2Match() | ||
| 63 |