How can I write my own function to compute automatically between clinical features and genes in R

Question

I'm trying to write my own function in R whose role is to automatically compute the correlation between genes and clinical features of interest. This is my code lines:

#Empty data.frame
cc1 <- data.frame(Estimate=paste("Site", 1:35), P.value="")
estimates = numeric(35)
pvalues = numeric(35)

#compute correlation between clinical feature and genes
computeCC = function(x)
{
  if (x = ""){
  for (i in 1:35) {
      cc<-cor.test(cor[,i], cor[,x],    
                   method = "spearman")
      estimates[i] = cc$estimate
      pvalues[i] = cc$p.value
      cc1$Estimate <- estimates
      cc1$P.value <- pvalues
      rownames(cc1) = colnames(cor)[1:35]}}}

in which, cor is a data frame including 1904 patients and 38 columns (35 genes + "lymph", "npi" and "stage"); "lymph", "npi" and "stage" are column names in cor and are three clinical features, i.e., number of positive lymph nodes, Nottingham prognostic index and tumor stage, respectively.

I'm wanting to write a function so that when I write something like:

computeCC(lymph)

It will show me the correlation coefficient and p-value between numbers of lymph nodes and each of 35 gene.

Similarly, when I write: computeCC(stage)

It will show me the correlation coefficient and p-value between tumor stage and each of 35 gene.

But right now, I have been running into a problem:

Error: unexpected '}' in: " cc1$P.value <- pvalues rownames(cc1) = colnames(cor)[1:35]}}"

This is my reproducible data:

cor <-  structure(list(NCOR1 = c(0.6488, 0.3312, -0.3336, 0.2663, -1.3986), ZFP36L1 = c(-1.4278, -1.9684, -1.4047, -1.1984, 0.397), SMAD4 = c(-0.5692, -2.5897, -1.4175, -2.2613, 0.6804), CDKN1B = c(-0.9829, -1.7246, -1.1409, -1.5033, -0.8475), CDH1 = c(-0.1387, 1.5924, -0.7637, 1.2737, 0.5298), PIK3R1 = c(0.2649, -0.2267, -0.6875, -0.8364, 1.3622), BRCA2 = c(0.6442, 1.2209, -0.6712, -1.0785, -0.296), KMT2C = c(-0.8759, -0.327, -0.0154, -0.7076, -0.0817), KRAS = c(0.5975, -0.0729, 0.0069, -1.3664, -0.9904), MUC16 = c(0.4375, -0.7318, -0.5569, -0.8224, -0.3882), CBFB = c(-0.9757, 0.9849, -0.9263, -1.7691, -0.7777), MAP2K4 = c(0.385, -0.6192, -1.5389, -0.1092, -2.4083), AHNAK2 = c(0.69, 0.2453, -0.0492, -1.0581, -0.2553), BAP1 = c(0.0535, -3.1571, 1.8473, -0.2338, -0.9715), ERBB2 = c(0.6171,4.4808, -0.643, 0.496, 1.1611), TP53 = c(-0.065, 1.3605, -0.0393, 1.6328, -0.3413), MAP3K1 = c(-1.241, -0.6619, -1.4874, -2.1246, 2.2862), ERBB3 = c(0.7237, -0.1072, -0.2926, -1.1115,0.5288), PTEN = c(-0.4454, -1.2554, -0.9175, -0.6936, -0.0996
), PIK3CA = c(-1.9252, -2.2674, -0.0451, -0.6883, -1.0361
), GPS2 = c(0.489, -0.363, 0.1914, -0.1519, 0.237), SF3B1 = c(1.0353, 
1.0428, 0.1198, -0.1978, 1.3932), AGTR2 = c(0.395, 1.7066, 
0.2963, 0.5277, 0.5876), SYNE1 = c(0.1814, -0.8717, -0.3925, 
-0.6181, 0.2515), GATA3 = c(0.727, -0.1693, 0.1266, 0.2467, 
0.7005), AKT1 = c(0.7579, 1.9675, -1.0293, -1.1985, -1.902
), FOXO3 = c(-0.1501, 0.0589, -0.3752, -0.4585, -0.8405), 
ARID1A = c(0.7732, -0.695, 0.0034, -0.9322, 0.5824), RB1 = c(-0.135, 
-0.6994, 0.487, 1.7919, 0.9048), CDKN2A = c(0.0647, 0.1072, 
-0.3117, -0.2668, -0.6555), MEN1 = c(-0.5376, 2.164, 1.2287, 
0.5037, 0.7852), NF1 = c(-0.5943, -0.2639, -0.8211, 0.2209, 
1.5184), TBX3 = c(-0.765, -0.2696, 0.1784, 0.6917, 0.3603
), CHEK2 = c(-0.5534, 1.8462, -0.8928, 0.7362, -0.3503), 
RUNX1 = c(-0.8007, -1.9473, 0.6226, -0.6965, 0.1434), lymph = c(1, 
5, 8, 1, 0), npi = c(4.036, 6.032, 6.03, 5.042, 3.046), stage = c(2, 
2, 3, 2, 2)), row.names = c("MB-0362", "MB-0346", "MB-0386", "MB-0574", "MB-0503"), class = "data.frame")

Can anyone suggest me an idea? Thanks in advance.

Hard to tell. The error is simply an off bracket somewhere. Could you share your data with dput(head(df,n))? — NelsonGon
Yeah, sure, sir. drive.google.com/drive/u/0/my-drive df<-read.table('df.txt', sep = '\t', check.names = FALSE, header = TRUE, row.names = NULL) — Huy Nguyen
Please provide the first 5 lines of the data as suggestet by @NelsonGon. Use the function dput() for this. — MKR
Hi Huy Nguyen. Welcome to StackOverflow! I see that you are struggling with providing good example data in a format that is usable for others that want to help you. Please read the info about how to ask a good question and how to give a minimale reproducible example. That way you can help others to help you! — dario
I have just provide reproducible data already. Sorry for my fault! @MKR — Huy Nguyen

Edward Edward · Accepted Answer · 2020-02-24T11:13:50

Try this. Your code has a number of problems. I have minimally modified it to (I think) get what you wanted.

computeCC = function(data, var) # Pass the data and a variable
{
  var <- eval(substitute(var), data, parent.frame()) # This may confuse you

  for (i in 1:35) {
    cc <- cor.test(data[,i], var, method = "spearman")
    estimates[i] = cc$estimate
    pvalues[i] = cc$p.value
  }

# These belong outside the loop
  cc1$Estimate <- estimates
  cc1$P.value <- pvalues
  rownames(cc1) = colnames(cor)[1:35]
  cc1
}

Then you call it and save the results:

cc2 <- computeCC(cor, lymph)

And then look at the results in cc2.

There are other changes that could be made to improve the code, but one step at a time.

Data provide by you:

cc1 <- data.frame(Estimate=paste("Site", 1:35), P.value="")
estimates = numeric(35)
pvalues = numeric(35)

How can I write my own function to compute automatically between clinical features and genes in R

3 Answers