goseq package in R "missing value where TRUE/FALSE needed" error - r

Question

I am attempting to run a GO Analysis in R (I have never done this analysis, so I am trying different packages), and I am struggling to find the problem with my code in the goseq package.
I start with this code which produces a list of the differentially expressed gene names:
de.genes <- rownames(res)[ which(res$padj < fdr.threshold & !is.na(res$padj)) ]
Then I try to run this code (based on page 7 of the vignette (https://bioconductor.org/packages/devel/bioc/vignettes/goseq/inst/doc/goseq.pdf)
pwf <- nullp(de.genes, "hg38","geneSymbol")
but I get the following error:
Can't find hg38/geneSymbol length data in genLenDataBase...
Found the annotation package, TxDb.Hsapiens.UCSC.hg38.knownGene
Trying to get the gene lengths from it.
Error in if (matched_frac == 0) { : missing value where TRUE/FALSE needed
In addition: Warning message:
In grep(txdbPattern, installedPackages):argument 'pattern' has length > 1 and only the first element will be used
I found this forum: https://support.bioconductor.org/p/38580/ that says I need an "indicator variable" but I do not know what this is.
Any help with this error would be greatly appreciated, or if you know of any other GO packages that are easy to learn. Thanks!

Answer 1

You can check the supported databases, hg38 is not one of them:
library(org.Hs.eg.db)
library(goseq)
supported[grep("hg38|hg19",supported$Genome),]
Genome Id Id Description Lengths in geneLeneDataBase
4 hg19 knownGene Entrez Gene ID TRUE
36 hg19 ensGene Ensembl gene ID TRUE
81 hg19 geneSymbol Gene Symbol TRUE
98 hg38 FALSE
GO Annotation Available
4 TRUE
36 TRUE
81 TRUE
98 TRUE
You can get a rough idea of what it looks like by using hg19, you will have some missing or unmatched by should be ok. You need to have a binary vector and it should be named, for example:
set.seed(111)
allgenes = keys(org.Hs.eg.db,keytype="SYMBOL")
de.genes = rbinom(100,1,0.3)
names(de.genes) = sample(allgenes,100)
It looks like this:
GALNT5 TPRKB CD48 OR52R1 LOC105372708 LOC112163649
0 1 0 0 0 0
LOC105369203 LOC110121115 LOC105377654 LOC105371502 LOC101929964 HPC14
0 0 0 0 0 0
IGHD4-17 LOC101927993 HINT1 BCC3 RPL18P3 LOC108281192
0 0 0 0 0 1
RNU6-793P JUN
0 0
This will be ok:
res = nullp(de.genes,"hg19","geneSymbol")