Custom reference giving "not available in GenomicDistributions package or GenomicDistributionsData package" error using calcPartitionsRef

[nmichaels89]

Hi, I am having an issue with using a custom reference. Here is my code and the error.

library("GenomicDistributions")
library("GenomicDistributionsData")
setwd('/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/GenomicDistributions/methyltest')

queryFile = system.file("methyltest", "all10_uniq.bed.gz", package="GenomicDistributions")
query = rtracklayer::import(queryFile)

fastaSource = "Glycine_max.Glycine_max_v2.1.dna.toplevel.fa.gz"
gtfSource = "Glycine_max.Glycine_max_v2.1.60.chr.gff3.gz"

features = c("gene", "exon", "three_prime_utr", "five_prime_utr")
GmaxGeneModels = getGeneModelsFromGTF(source=gtfSource, features=features, convertEnsemblUCSC=TRUE)
partitionList = genomePartitionList(GmaxGeneModels$gene, 
                                    GmaxGeneModels$exon,
                                    GmaxGeneModels$three_prime_utr, 
                                    GmaxGeneModels$five_prime_utr)

gp = calcPartitionsRef(query, "GmaxGeneModels")
plotPartitions(gp)

The error is:

Error in getGeneModels(refAssembly) : 
  geneModels_GmaxGeneModels not available in GenomicDistributions package or GenomicDistributionsData package, 
please use getGeneModelsFromGTF() to get gene models.

Please let me know if there is something I am doing wrong. I can provide any needed information.

[kkupkova]

Hi! To use the function with a custom genome, you then pass the created partition list to the calcPartitions function (without "Ref" at the end - the functions with "Ref" expect an existing reference within the package):
gp = calcPartition(query, partitionList)

[nmichaels89]

Hi, thank you so much for the fast response! These commands do run, but 100% of the locations are distributed in the intergenic category. My input BED file is marking epigenetic modifications, so the regions are only one base long. Could this be causing the issue? Thank you again