A bug or a problem when using ChIPseeker to do genomic annotation ?

[Xiangyi-Deng]

Hello Dr. Yu,

I met a problem about ChIPseeker recently.

I used this package on different environment, including the virtual PC and linux server.

Because there are different versions of the same packages which are necessary fo the genomic annoation.

At the beginning, I didn't focus on versions.

But I got different genomic annotation results. And one result of them seemed wrong.

Here is my script that I used to do genomic annotation.

In order to confirm this bug or problem that was not caused by other unrelated packages, here I just load necessary packages.

And the session infomation is attached here.

library(ChIPseeker)
library(GenomicRanges)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
txdb <-TxDb.Hsapiens.UCSC.hg38.knownGene
library(IRanges)

#head(tile_set)
tile_set <- df_methylObject2

# vec_randomNum <- runif(length(vec_DMRs), min = 0, max = 1)
gr_total <- GRanges(seqnames = tile_set$seqnames, strand = tile_set$strand,
                    ranges = IRanges(start = as.numeric(tile_set$start), width = 500))
values(gr_total) <- DataFrame(V5 = as.numeric(as.character(tile_set$V5)))

library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)

txdb <-TxDb.Hsapiens.UCSC.hg38.knownGene
peakAnno <- annotatePeak(gr_total, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db")

The first version is used on my virtual PC:

**R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] org.Hs.eg.db_3.16.0 TxDb.Hsapiens.UCSC.hg38.knownGene_3.13.0 GenomicFeatures_1.50.4
[4] AnnotationDbi_1.60.2 Biobase_2.58.0 GenomicRanges_1.50.2
[7] GenomeInfoDb_1.34.9 IRanges_2.32.0 S4Vectors_0.36.2
[10] BiocGenerics_0.44.0 ChIPseeker_1.34.1**

And on my linux serverv(Rstudio online), it is:

sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] org.Hs.eg.db_3.16.0 TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0 GenomicFeatures_1.52.0
[4] AnnotationDbi_1.60.2 Biobase_2.58.0 ChIPseeker_1.36.0
[7] methylKit_1.24.0 GenomicRanges_1.50.2 GenomeInfoDb_1.36.0
[10] IRanges_2.32.0 S4Vectors_0.36.2 BiocGenerics_0.44.0

I have checked these necessary packages version.

Especially TxDb.Hsapiens.UCSC.hg38.knownGene, GenomicFeatures, ChIPseeker, GenomeInfoDb

I don't know which one caused this bug or problem.

Because of data protection in Germany, forgive me that I cannot post my data here.

But I hope you can focus on this problem or I also hope I did it by mistake.

Thanks in advance.

Best,
xiangyi