Help in my coding for network analysis

[amare]

Hi Dear friends
I would like to ask for coding help here. I am doing a correlation between two data matrices (A and B). For each pair of correlations, I want to filter the significant ones based on the p-value. Then, I would like to compare each correlated pairs with another data frame containing the target pair variable. Therefore, if the correlated pairs belong to the target pair variable I will code 1 otherwise zero on another column.

The data look below

 set.seed(42)
 B <- matrix(rnorm(1000), nrow = 100)
 rownames(B) <- paste0("m_", ncol = 1:100)
 colnames(B) <- paste0("S_", ncol = 1:10)
 set.seed(145)
 A <- matrix(rnorm(1000), nrow = 100)
 rownames(A) <- paste0("g_", ncol = 1:100)
 colnames(A) <- paste0("S_", ncol = 1:10)

targetlist <- data.frame(g = sample(rownames(A),50), m = sample(rownames(B),50))
 library(dplyr)
 sig_correlation2Dfs<-function(A,B){
  n <- t(!is.na(A)) %*% (!is.na(B)) 
   r <- cor(A, B, use = "pairwise.complete.obs") 
   cor2pvalue = function(r, n) {
     t <- (r*sqrt(n-2))/sqrt(1-r^2) ## t-distribution 
     p <- 2*(1 - pt(abs(t),(n-2))) ## pvalue
     out <- list(r, n, t, p)
     names(out) <- c("r", "n", "t", "p")
     return(out)
   }
   
   # Get a list with matrices of correlation, pvalues
   result = cor2pvalue(r,n)
   rcoeffMatrix<-result$r
   pvalueMatrix<-result$p
   rows<-rownames(rcoeffMatrix)
   cols<-colnames(pvalueMatrix)
   df <- data.frame(A=character(),
                    B=character(), 
                    cor=double(),
                    Pvalue=double(),
                    stringsAsFactors=FALSE) 
   
   for(i in rows){
     for(j in cols){
       if (pvalueMatrix[i,j] > 0.05){
         next
       }else{
         cor<-rcoeffMatrix[i,j]
         Pvalue<-pvalueMatrix[i,j]
         df<- df %>% add_row(A = i, B = j, cor = cor, Pvalue = Pvalue)
       }
     }
   }
   df
 }
 xx <- sig_correlation2Dfs(t(A), t(B))

Now, if the correlated variables(e.g g_1 and m_1 pair) simlatinouesly belong in the target list as g_1 and m_1 pair, I want to code 1 otherwise zero. Overall the final output I would like to have is as indicated in the picture below.

Best,
Amare

[gtmbini]

I am not quite sure if this something you want. But, you can see I have given two different types of solutions, first exactly like what you showed. I just put two datasets together side by side not considering anything and add an indicator variable if xx data set A, B matches to g m of another dataset. I think there were 4 of them that matched.

I also tried the merge approach. You see if there is no NA in a row that means the pair are present in two datasets otherwise they are in either of one xx or target. But they are not put together.

#####
library(tidyverse)
set.seed(42)
B <- matrix(rnorm(1000), nrow = 100)
rownames(B) <- paste0("m_", ncol = 1:100)
colnames(B) <- paste0("S_", ncol = 1:10)
set.seed(145)
A <- matrix(rnorm(1000), nrow = 100)
rownames(A) <- paste0("g_", ncol = 1:100)
colnames(A) <- paste0("S_", ncol = 1:10)

targetlist <- data.frame(g = sample(rownames(A),50), m = sample(rownames(B),50))
library(dplyr)
sig_correlation2Dfs<-function(A,B){
  n <- t(!is.na(A)) %*% (!is.na(B)) 
  r <- cor(A, B, use = "pairwise.complete.obs") 
  cor2pvalue = function(r, n) {
    t <- (r*sqrt(n-2))/sqrt(1-r^2) ## t-distribution 
    p <- 2*(1 - pt(abs(t),(n-2))) ## pvalue
    out <- list(r, n, t, p)
    names(out) <- c("r", "n", "t", "p")
    return(out)
  }
  
  # Get a list with matrices of correlation, pvalues
  result = cor2pvalue(r,n)
  rcoeffMatrix<-result$r
  pvalueMatrix<-result$p
  rows<-rownames(rcoeffMatrix)
  cols<-colnames(pvalueMatrix)
  df <- data.frame(A=character(),
                   B=character(), 
                   cor=double(),
                   Pvalue=double(),
                   stringsAsFactors=FALSE) 
  
  for(i in rows){
    for(j in cols){
      if (pvalueMatrix[i,j] > 0.05){
        next
      }else{
        cor<-rcoeffMatrix[i,j]
        Pvalue<-pvalueMatrix[i,j]
        df<- df %>% add_row(A = i, B = j, cor = cor, Pvalue = Pvalue)
      }
    }
  }
  df
}
xx <- sig_correlation2Dfs(t(A), t(B))

targetlist$g<- as.character(targetlist$g)
targetlist$m<- as.character(targetlist$m)


i1 <- match(paste(xx$A, xx$B), paste(targetlist$g, targetlist$m), nomatch = 0)
i1[i1>1] = 1

library(qpcR)
#> Loading required package: MASS
#> 
#> Attaching package: 'MASS'
#> The following object is masked from 'package:dplyr':
#> 
#>     select
#> Loading required package: minpack.lm
#> Loading required package: rgl
#> Loading required package: robustbase
#> Loading required package: Matrix
#> 
#> Attaching package: 'Matrix'
#> The following objects are masked from 'package:tidyr':
#> 
#>     expand, pack, unpack
merge<- qpcR:::cbind.na(xx, targetlist)
merge$gmpair<- i1

merge [1:15,]
#>      A    B        cor      Pvalue    g    m gmpair
#> 1  g_1  m_1  0.7014863 0.023777696  g_7 m_54      0
#> 2  g_1 m_11  0.6542419 0.040136845 g_34 m_42      0
#> 3  g_1 m_30 -0.6608990 0.037473787 g_28  m_6      0
#> 4  g_1 m_57  0.8268228 0.003174772 g_16  m_1      0
#> 5  g_1 m_84 -0.7585984 0.010971358 g_77 m_37      0
#> 6  g_2 m_35  0.7309656 0.016317876 g_66  m_9      0
#> 7  g_2 m_54  0.6626535 0.036792338 g_44 m_64      0
#> 8  g_2 m_86 -0.8376313 0.002487474 g_72 m_28      0
#> 9  g_2 m_92 -0.6982939 0.024704891 g_12 m_71      0
#> 10 g_3 m_56 -0.7484422 0.012765535 g_32 m_15      0
#> 11 g_3 m_62  0.6412703 0.045685764  g_3  m_3      0
#> 12 g_3 m_63  0.6505131 0.041682715 g_81 m_94      0
#> 13 g_3 m_68  0.7852333 0.007117049 g_18 m_32      0
#> 14 g_3 m_75 -0.7357742 0.015279416 g_55 m_29      0
#> 15 g_3 m_88 -0.6469525 0.043195695 g_91 m_65      0

# Another method
xx$ID1<- as.character(xx$A)
xx$ID2<- as.character(xx$B)

targetlist$ID1<- as.character(targetlist$g)
targetlist$ID2<- as.character(targetlist$m)


merge.file<- merge(xx, targetlist, by= c("ID1", "ID2"), all = TRUE )
merge.file$gmpair<-  ifelse(complete.cases(merge.file)==1, 1,0)     
merge.file<- merge.file %>% dplyr::select(-c(ID1, ID2))
merge.file[1:30,]
#>        A    B        cor       Pvalue    g    m gmpair
#> 1    g_1  m_1  0.7014863 0.0237776960 <NA> <NA>      0
#> 2    g_1 m_11  0.6542419 0.0401368454 <NA> <NA>      0
#> 3    g_1 m_30 -0.6608990 0.0374737872 <NA> <NA>      0
#> 4    g_1 m_57  0.8268228 0.0031747724 <NA> <NA>      0
#> 5    g_1 m_84 -0.7585984 0.0109713582 <NA> <NA>      0
#> 6   g_10 m_13 -0.9057432 0.0003077797 <NA> <NA>      0
#> 7   g_10 m_14 -0.8999465 0.0003879589 <NA> <NA>      0
#> 8   g_10 m_32 -0.6547675 0.0399220998 <NA> <NA>      0
#> 9   g_10 m_40  0.6407355 0.0459249438 <NA> <NA>      0
#> 10  g_10 m_47  0.7228194 0.0181874913 <NA> <NA>      0
#> 11  <NA> <NA>         NA           NA g_10 m_79      0
#> 12  g_10 m_83 -0.7845922 0.0071963977 <NA> <NA>      0
#> 13 g_100 m_32  0.6345359 0.0487590474 <NA> <NA>      0
#> 14 g_100 m_46 -0.6374117 0.0474302990 <NA> <NA>      0
#> 15 g_100 m_67  0.6602530 0.0377268136 <NA> <NA>      0
#> 16 g_100 m_73  0.8017408 0.0052803843 <NA> <NA>      0
#> 17 g_100 m_86  0.6658360 0.0355776974 <NA> <NA>      0
#> 18  g_11 m_12 -0.6338640 0.0490730266 <NA> <NA>      0
#> 19  g_11 m_45  0.7271768 0.0171699107 <NA> <NA>      0
#> 20  g_11 m_67  0.6687339 0.0344955594 <NA> <NA>      0
#> 21  g_11  m_8  0.7732543 0.0087056588 <NA> <NA>      0
#> 22  g_11 m_96  0.7467191 0.0130890753 <NA> <NA>      0
#> 23  g_11 m_97  0.7724212 0.0088246927 <NA> <NA>      0
#> 24  g_12  m_1 -0.6434832 0.0447049110 <NA> <NA>      0
#> 25  g_12  m_2  0.6809475 0.0301796889 <NA> <NA>      0
#> 26  g_12 m_22  0.7979446 0.0056686682 <NA> <NA>      0
#> 27  g_12 m_43 -0.6561107 0.0393767892 <NA> <NA>      0
#> 28  g_12  m_7 -0.6621928 0.0369704595 <NA> <NA>      0
#> 29  <NA> <NA>         NA           NA g_12 m_71      0
#> 30  g_12  m_9 -0.7006940 0.0240055301 <NA> <NA>      0

[amare]

@gtmbini ,

Thank you so much for your prompt answer. I appreciated it.
However, I wonder if each pair(e.g., g_1 and m_1 pair in the column A and B) compared to all pairs in the column g and m. Because for g_1 and m_1 pair in column A and B, you might have g_1 and m_1 pair in column g and m somewhere, for example, in the row number 10000.

Best,
Amare

[gtmbini]

Yes, each paired in XX data was checked with all pairs in the target dataset. The match function that I used checks every pair of A and B if exists in the g and m and gives you the index in which position it exists in the g and m dataset, if there is no match it writes 0. You can see in the code, for i1 variable I replace all the values greater than 1 with 1. To have 0 and 1 for pair value. If I recall correctly, there were only 4 that were in xx matched in target data.