Target gene assignment in vignette: Problem with "_PAR_Y"

[MelinaKlostermann]

Hello,
I am using your vignette (https://www.bioconductor.org/packages/release/bioc/vignettes/BindingSiteFinder/inst/doc/vignette.html) and found and got an Error in the " Target gene assignment" part (with gencode.v31.annotation.gff3):

> annoDb = makeTxDbFromGFF(file = mygff3, format = "gff3")
> annoInfo = import(mygff3, format = "gff3")
> 
> # Get genes as GRanges
> gns = genes(annoDb)
> idx = match(gns$gene_id, annoInfo$gene_id)
> elementMetadata(gns) = cbind(elementMetadata(gns),
+                              elementMetadata(annoInfo)[idx,])

Error: subscript contains NAs

The problems seem to be the _PAR_Y gene names.

gns$gene_id[!(gns$gene_id %in% annoInfo$gene_id)]

[1] "ENSG00000002586.20_PAR_Y" "ENSG00000124333.16_PAR_Y" "ENSG00000124334.17_PAR_Y" "ENSG00000167393.17_PAR_Y" "ENSG00000168939.11_PAR_Y" "ENSG00000169084.14_PAR_Y"
[7] "ENSG00000169093.16_PAR_Y" "ENSG00000169100.14_PAR_Y" "ENSG00000178605.13_PAR_Y" "ENSG00000182162.11_PAR_Y" "ENSG00000182378.14_PAR_Y" "ENSG00000182484.15_PAR_Y"
[13] "ENSG00000185203.12_PAR_Y" "ENSG00000185291.11_PAR_Y" "ENSG00000185960.14_PAR_Y" "ENSG00000196433.13_PAR_Y" "ENSG00000197976.12_PAR_Y" "ENSG00000198223.16_PAR_Y"
[19] "ENSG00000205755.11_PAR_Y" "ENSG00000214717.12_PAR_Y" "ENSG00000223274.6_PAR_Y" "ENSG00000223484.7_PAR_Y" "ENSG00000223511.7_PAR_Y" "ENSG00000223571.6_PAR_Y"
[25] "ENSG00000223773.7_PAR_Y" "ENSG00000225661.7_PAR_Y" "ENSG00000226179.6_PAR_Y" "ENSG00000227159.8_PAR_Y" "ENSG00000228410.6_PAR_Y" "ENSG00000228572.7_PAR_Y"
[31] "ENSG00000229232.6_PAR_Y" "ENSG00000230542.6_PAR_Y" "ENSG00000234622.6_PAR_Y" "ENSG00000234958.6_PAR_Y" "ENSG00000236017.8_PAR_Y" "ENSG00000236871.7_PAR_Y"
[37] "ENSG00000237040.6_PAR_Y" "ENSG00000237531.6_PAR_Y" "ENSG00000237801.6_PAR_Y" "ENSG00000265658.6_PAR_Y" "ENSG00000270726.6_PAR_Y" "ENSG00000275287.5_PAR_Y"
[43] "ENSG00000277120.5_PAR_Y" "ENSG00000280767.3_PAR_Y" "ENSG00000281849.3_PAR_Y"

A solution is to remove the _PAR. Maybe include that in the vignette?

annoDb = makeTxDbFromGFF(file = mygff3, format = "gff3")
annoInfo = import(mygff3, format = "gff3")

# Get genes as GRanges
gns = genes(annoDb)
gns = gns[!grepl(pattern = "_PAR_Y", gns$gene_id)]
idx = match(gns$gene_id, annoInfo$gene_id)
elementMetadata(gns) = cbind(elementMetadata(gns),
                             elementMetadata(annoInfo)[idx,])

[MirkoBr]

This fixed with the latest major update on our way to version 2.0. See commit 80de317