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mictadlo
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@mictadlo-10885
Last seen 4.9 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.
Your "
geneID2GO" doesn't look well, it has double quotes, have you triedremoving one pair of quotes from the characters? This way the`"sp0000017"` will become"sp0000017" and thus will be mapped with the geneList.Also theGOs:"\"GO:0004672" "GO:0005524" "GO:0006468\"", should be splited by space.The
GOmapping.tsvlooks like this:How is possible to fix the problem with the quotes and spaces?
Thank you in advance.
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.