Hello,
I am trying to write a code in R to get the GO label has the highest confident score that comes after " | " symbol
For each gene ID (each row), there are many Go labels (columns), it can go up to 400 labels. And the Go-term with highest confident score can be in any column.
see example:
GeneID GO_01 GO_02 GO_03 GO_04
exi2A01G0001540.1 GO:0005575|0.853 GO:0005622|0.705 GO:0005623|0.846 GO:0005634|0.531
exi2A01G0001560.1 GO:0005575|0.324 GO:0044699|0.319 GO:0044464|0.324 GO:0005623|0.524
exi9A01G0045270.1 GO:0003674|0.356 GO:0005575|0.679 GO:0005622|0.539
I think it's possible to retain the GO-labels that has the highest confident score.
So for example results would be like this:
GeneID GO-term
exi2A01G0001540.1 GO:0005575|0.853
exi2A01G0001560.1 GO:0005623|0.524
exi9A01G0045270.1 GO:0005575|0.679
I srarted R code:
GO_1 <- read.table("proteinGO-term_0.3.txt", header=T, sep="\t", fill=T)
#have gene ID as a row name:
GO_2 <- GO_1[,-1]
rownames(GO_2) <- GO_1[,1]
#
#I tried this, but it doesn't do what I want:
test <- apply(GO_2,1,function(x) which(x==max(x)))
Thanks !!!
2 answers
> cbind(test[,1],(t(apply(test[,-1],1, function(x) x[order(as.numeric(sub("\\w*:[0-9]*\\|","",x)),decreasing = T)]))))[,1:2]
[,1] [,2]
[1,] "exi2A01G0001540.1" "GO:0005575|0.853"
[2,] "exi2A01G0001560.1" "GO:0005623|0.524"
[3,] "exi9A01G0045270.1" "GO:0005575|0.679"
Please post the example data. Code works on the data furnished in OP. If you are concerned about column names, you can do this:
$ cbind("GeneID"=test[,1],"GO-term"=apply(test[,-1],1, function(x) x[order(as.numeric(sub("\\D+\\d+\\D","",x)),decreasing = T)][1]))
GeneID GO-term
[1,] "exi2A01G0001540.1" "GO:0005575|0.853"
[2,] "exi2A01G0001560.1" "GO:0005623|0.524"
[3,] "exi9A01G0045270.1" "GO:0005575|0.679"
Yeah you are right head(test[,1])
Showed me the gene ID, but I have no idea, running the whole line, doesn't show the gene ID
but anyway the good thing now it worked when making the first column as row names
However, there is another problem. When a gene has only one GO-term, it leaves it empty. But it should retain that only Go-label for the corresponding gene. right?
sure. It should do so. It also depends on you are reading input (txt) file in to R. I have created example file, where the GO term is present in only column, but absent in all other columns, for few GO columns. Follow the code below:
$ cat GO_test.txt
GeneID GO_01 GO_02 GO_03 GO_04
gene1 GO:0005575|0.853 GO:0005622|0.705 GO:0005623|0.846 GO:0005634|0.531
gene2 GO:0005575|0.324 GO:0044699|0.319 GO:0044464|0.324 GO:0005623|0.524
gene3 GO:0003674|0.356 GO:0005575|0.679 GO:0005622|0.539
gene4 GO:0005622|0.539
gene5 GO:0005575|0.679
gene6 GO:0005575|0.679
Gene 4 has entry in third column and all other columns are empty. Gene 5 has entry in 2nd column and all other columns are empty. Gene 6 has entry in 1st column and all other columns are empty. Here is the R code:
> test=read.csv("GO_test.txt", header = T, sep = "\t", strip.white = T, na.strings = "")
> test
GeneID GO_01 GO_02 GO_03 GO_04
1 gene1 GO:0005575|0.853 GO:0005622|0.705 GO:0005623|0.846 GO:0005634|0.531
2 gene2 GO:0005575|0.324 GO:0044699|0.319 GO:0044464|0.324 GO:0005623|0.524
3 gene3 GO:0003674|0.356 GO:0005575|0.679 GO:0005622|0.539 <NA>
4 gene4 <NA> <NA> GO:0005622|0.539 <NA>
5 gene5 <NA> GO:0005575|0.679 <NA> <NA>
6 gene6 GO:0005575|0.679 <NA> <NA> <NA>
> cbind("GeneID"=test[,1],"GO-term"=apply(test[,-1],1, function(x) x[order(as.numeric(sub("\\D+\\d+\\D","",x)),decreasing = T)][1]))
GeneID GO-term
[1,] "gene1" "GO:0005575|0.853"
[2,] "gene2" "GO:0005623|0.524"
[3,] "gene3" "GO:0005575|0.679"
[4,] "gene4" "GO:0005622|0.539"
[5,] "gene5" "GO:0005575|0.679"
[6,] "gene6" "GO:0005575|0.679"
Given the data.frame was called example.data:
output <- lapply(1:nrow(example.data), function(x){
tmp <- as.character(example.data[x,2:ncol(example.data)])
tmp.max <- sort(sapply(strsplit(tmp, split = "\\|"), function(x) x[2]),
decreasing = TRUE, index.return = TRUE)$ix[1]
data.frame(GeneID = example.data[x,1], `GO-term` = example.data[x,tmp.max+1])
})
output <- do.call(rbind, is.max)
Thanks a lot!
This line in the code gives an error, although everything seems to be ok
data.frame(GeneID = example.data[x,1], `GO-term` = example.data[x,tmp.max+1])
Error in data.frame(GeneID = example.data[x, 1],
GO-term= example.data[x, : arguments imply differing number of rows: 1, 0
When tracing the error:
5. stop(gettextf("arguments imply differing number of rows: %s",
paste(unique(nrows), collapse = ", ")), domain = NA)
4. data.frame(GeneID = example.data[x, 1], `GO-term` = example.data[x,
tmp.max + 1])
3. FUN(X[[i]], ...)
2. lapply(1:nrow(example.data), function(x) {
tmp <- as.character(example.data[x, 2:ncol(example.data)])
tmp.max <- sort(sapply(strsplit(tmp, split = "\\|"), function(x) x[2]),
decreasing = TRUE, index.return = TRUE)$ix[1] ...
1. lapply(1:nrow(example.data), function(x) {
tmp <- as.character(example.data[x, 2:ncol(example.data)])
tmp.max <- sort(sapply(strsplit(tmp, split = "\\|"), function(x) x[2]),
decreasing = TRUE, index.return = TRUE)$ix[1] ...
The data look like this, the same one I posted in the question as an example
with or without putting the first column as row names, I get the same error
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