Commit 78589c8b87579fcf191fc35f9d803f75e336a2fa
1 parent
eb003daf3f
Exists in
master
Updated output question
Showing
1 changed file
with
1 additions
and
1 deletions
Show diff stats
RMatchGenes.R
1 | #Checking for similar genes in both data sets | 1 | #Checking for similar genes in both data sets |
2 | 2 | ||
3 | #Required libraries | 3 | #Required libraries |
4 | library(MASS) | 4 | library(MASS) |
5 | library(readr) | 5 | library(readr) |
6 | library(dplyr) | 6 | library(dplyr) |
7 | 7 | ||
8 | Check2Match <- function(){ | 8 | Check2Match <- function(){ |
9 | numrows <- "How many rows of clinical data are their in the each data set?: " %>% | 9 | numrows <- "How many rows of clinical data are their in the each data set (seperate each number by a comma no spaces)?: " %>% |
10 | readline(prompt = .) %>% | 10 | readline(prompt = .) %>% |
11 | strsplit(.,split = ",") %>% | 11 | strsplit(.,split = ",") %>% |
12 | .[[1]] %>% | 12 | .[[1]] %>% |
13 | as.integer(.) | 13 | as.integer(.) |
14 | i <- 1 | 14 | i <- 1 |
15 | ANDIS <- select.list(choices = list.files(),multiple = TRUE, title = "Choose the file/files you want to analyze:") | 15 | ANDIS <- select.list(choices = list.files(),multiple = TRUE, title = "Choose the file/files you want to analyze:") |
16 | 16 | ||
17 | for(i in 1:length(numrows)){ | 17 | for(i in 1:length(numrows)){ |
18 | if( i == 1){ | 18 | if( i == 1){ |
19 | edfile <- ANDIS[i] | 19 | edfile <- ANDIS[i] |
20 | ed <- edfile %>% | 20 | ed <- edfile %>% |
21 | read_delim(.,delim = "\t") | 21 | read_delim(.,delim = "\t") |
22 | ednocd <- ed[-(1:numrows[1]),] | 22 | ednocd <- ed[-(1:numrows[1]),] |
23 | #Second file brought in | 23 | #Second file brought in |
24 | eddfile <- ANDIS[i + 1] | 24 | eddfile <- ANDIS[i + 1] |
25 | edd <- eddfile %>% | 25 | edd <- eddfile %>% |
26 | read_delim(.,delim = "\t") | 26 | read_delim(.,delim = "\t") |
27 | eddnocd <- edd[-(1:numrows[2]),] | 27 | eddnocd <- edd[-(1:numrows[2]),] |
28 | 28 | ||
29 | ##Fully matched both data sets | 29 | ##Fully matched both data sets |
30 | eddy <- inner_join(ednocd,eddnocd) | 30 | eddy <- inner_join(ednocd,eddnocd) |
31 | #Matches | 31 | #Matches |
32 | meds <- eddy[,1] | 32 | meds <- eddy[,1] |
33 | 33 | ||
34 | } | 34 | } |
35 | if(i > 1 && i + 1 < length(numrows)){ | 35 | if(i > 1 && i + 1 < length(numrows)){ |
36 | eddfile <- ANDIS[i + 1] | 36 | eddfile <- ANDIS[i + 1] |
37 | edd <- eddfile %>% | 37 | edd <- eddfile %>% |
38 | read_delim(.,delim = "\t") | 38 | read_delim(.,delim = "\t") |
39 | eddnocd <- edd[-(1:numrows[i + 1]),] | 39 | eddnocd <- edd[-(1:numrows[i + 1]),] |
40 | ##Fully matched both data sets | 40 | ##Fully matched both data sets |
41 | eddy <- inner_join(meds,eddnocd) | 41 | eddy <- inner_join(meds,eddnocd) |
42 | meds <- eddy[,1] | 42 | meds <- eddy[,1] |
43 | 43 | ||
44 | 44 | ||
45 | } | 45 | } |
46 | i <- i + 1 | 46 | i <- i + 1 |
47 | } | 47 | } |
48 | meds | 48 | meds |
49 | for(j in 1:length(numrows)){ | 49 | for(j in 1:length(numrows)){ |
50 | edfile <- ANDIS[j] | 50 | edfile <- ANDIS[j] |
51 | ed <- edfile %>% | 51 | ed <- edfile %>% |
52 | read_delim(.,delim = "\t") | 52 | read_delim(.,delim = "\t") |
53 | ednocd <- ed[-(1:numrows[j]),] | 53 | ednocd <- ed[-(1:numrows[j]),] |
54 | #use meds to match | 54 | #use meds to match |
55 | eddy <- inner_join(meds,ednocd) | 55 | eddy <- inner_join(meds,ednocd) |
56 | Finedm <- rbind(ed[1:numrows[j],],eddy) | 56 | Finedm <- rbind(ed[1:numrows[j],],eddy) |
57 | nam_fil_ed <- strsplit(edfile,"[\\|/]") %>% | 57 | nam_fil_ed <- strsplit(edfile,"[\\|/]") %>% |
58 | .[[1]] %>% | 58 | .[[1]] %>% |
59 | .[length(.)] %>% | 59 | .[length(.)] %>% |
60 | gsub("\\D","",.) %>% | 60 | gsub("\\D","",.) %>% |
61 | c("GSE",.,"matched.txt") %>% | 61 | c("GSE",.,"matched.txt") %>% |
62 | paste(collapse = "") | 62 | paste(collapse = "") |
63 | write.table(Finedm,file = nam_fil_ed,sep = "\t",row.names = FALSE) | 63 | write.table(Finedm,file = nam_fil_ed,sep = "\t",row.names = FALSE) |
64 | j <- j + 1 | 64 | j <- j + 1 |
65 | } | 65 | } |
66 | meds | 66 | meds |
67 | } | 67 | } |
68 | 68 | ||
69 | Check2Match() | 69 | Check2Match() |