topGO - missing value where TRUE/FALSE needed
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mictadlo ▴ 10
@mictadlo-10885
Last seen 4.2 years ago

Hi,

I found here a tutorial how to use topGO. Unfortunately, I got missing value where TRUE/FALSE needed with the below code:

    > tr <- glmTreat(fit, contrast=B.LvsP, lfc=log2(1.5))
    > topTags(tr)
    Coefficient:  -1*Leaves.2 1*Leaves.3 
              logFC unshrunk.logFC logCPM  PValue     FDR
    sp0090975   2.6            2.6    2.8 5.7e-14 2.7e-09
    sp0037632  -3.0           -3.0    3.4 1.7e-13 2.7e-09
    sp0074153  -3.9           -3.9    3.8 1.8e-13 2.7e-09
    sp0008306   3.2            3.2    2.9 1.8e-13 2.7e-09
    sp0073530  -4.5           -4.5    3.4 2.3e-12 2.3e-08
    sp0025713  -3.9           -3.9    4.4 2.6e-12 2.3e-08
    sp0037721   7.8            8.0    2.4 2.7e-12 2.3e-08
    sp0083660   2.0            2.0    4.4 3.2e-12 2.3e-08
    sp0052245  -2.9           -2.9    4.9 3.9e-12 2.6e-08
    sp0071520  -3.3           -3.3    2.7 5.8e-12 3.4e-08

> geneID2GO <- readMappings(file = "~/GOmapping.tsv")
> head(geneID2GO)
$`"V1"`
[1] "\"V14\""

$`"sp0000005"`
[1] "\"GO:0003723\""

$`"sp0000006"`
[1] "\"GO:0016021\""

$`"sp0000007"`
[1] "\"GO:0003700" "GO:0006355"   "GO:0043565\""

$`"sp0000016"`
[1] "\"GO:0046983\""

$`"sp0000017"`
[1] "\"GO:0004672" "GO:0005524"   "GO:0006468\""

> 
> geneList <- tr$table$PValue
> names(geneList) <- rownames(tr)
> head(geneList)
   sp0025247    sp0025250    sp0025268    sp0025270    sp0025282    sp0056834 
9.891807e-01 4.062609e-01 9.633703e-01 1.037051e-03 9.633191e-05 6.661673e-01 
> 
> topDiffGenes = function(allScore) {
+   return (allScore < 1e-2)
+ }
> myGOdata <- new("topGOdata", 
+                 description="My project", 
+                 ontology="BP", 
+                 allGenes=geneList,
+                 geneSelectionFun = topDiffGenes,
+                 annot = annFUN.gene2GO, 
+                 gene2GO = geneID2GO)

Building most specific GOs .....
    ( 0 GO terms found. )

Build GO DAG topology ..........
    ( 0 GO terms and 0 relations. )
Error in if is.na(index) || index < 0 || index > length(nd)) stop("vertex is not in graph: ",  : 
  missing value where TRUE/FALSE needed

What did I miss?

Thank you in advance.

topgo edger • 2.5k views
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Your "geneID2GO" doesn't look well, it has double quotes, have you tried removing one pair of quotes from the characters? This way the `"sp0000017"` will become "sp0000017" and thus will be mapped with the geneList.

 

Also the GOs:"\"GO:0004672" "GO:0005524" "GO:0006468\"", should be splited by space.

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The GOmapping.tsv looks like this:

"V1"    "V14"
"sp0000005"    "GO:0003723"
"sp0000006"    "GO:0016021"
"sp0000007"    "GO:0003700,GO:0006355,GO:0043565"
"sp0000016"    "GO:0046983"
"sp0000017"    "GO:0004672,GO:0005524,GO:0006468"

How is possible to fix the problem with the quotes and spaces?

Thank you in advance.

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Entering edit mode

When reading the file with read.delim, check that the quote argument has the ". Also split the second column by comma. strsplit(",", x) where x would be each row in V14.

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