Thank you very much for this package! I seem to have an error in the annotatePeak output that I cannot find an existing issue about. I am using R version 4.1.2 and ChIPseeker_1.30.3. Here is the rest of the relevant session_info():
Here are a list of regions I want to annotate (small subset to illustrate the issue):
LALB_chr_3 2627151 2628080
LALB_chr_3 2659532 2660013
LALB_chr_3 2664362 2666431
And here are relevant proximal genes (just showing the "gene" entry from the gff3):
LALB_chr_3 maker gene 2623697 2633465 . - . ID=LALB_04121;Name=LALB_04121
LALB_chr_3 maker gene 2660123 2661437 . - . ID=LALB_04122;Name=LALB_04122
I would like to annotate a region as downstream if it is within 5000 bp of the end of the gene (on either strand). I found elsewhere on this site that I can use the options(ChIPseeker.downstreamDistance = 5000) to accomplish this. Here is what I run:
The second region is annotated as "Distal Intergenic", but it is only 110bp downstream from the gene LALB_04122. Even the default downstream distance (300, I think) should be greater than 110bp, so the options(ChIPseeker.downstreamDistance = 5000) should not matter here, although I do want to include regions that are within 5kb.
Happy to send files if needed or answer any other questions. Thank you!
Hello,
Thank you very much for this package! I seem to have an error in the annotatePeak output that I cannot find an existing issue about. I am using R version 4.1.2 and ChIPseeker_1.30.3. Here is the rest of the relevant session_info():
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale
LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
stats4 stats graphics grDevices utils datasets methods base
other attached packages:
ggimage_0.3.1 ggplot2_3.4.0 ggupset_0.3.0 GenomicFeatures_1.46.5 AnnotationDbi_1.56.2
Biobase_2.54.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.2
BiocGenerics_0.40.0 ChIPseeker_1.30.3
I have a custom genome/annotation, so I first make a txdb object from my gff3:
library(GenomicFeatures) test_txdb <- makeTxDbFromGFF(file="chr3_subset.gff3", dataSource="chr3_subset.gff3", organism="Lasioglossum albipes")
Here are a list of regions I want to annotate (small subset to illustrate the issue): LALB_chr_3 2627151 2628080 LALB_chr_3 2659532 2660013 LALB_chr_3 2664362 2666431
And here are relevant proximal genes (just showing the "gene" entry from the gff3): LALB_chr_3 maker gene 2623697 2633465 . - . ID=LALB_04121;Name=LALB_04121 LALB_chr_3 maker gene 2660123 2661437 . - . ID=LALB_04122;Name=LALB_04122
I would like to annotate a region as downstream if it is within 5000 bp of the end of the gene (on either strand). I found elsewhere on this site that I can use the options(ChIPseeker.downstreamDistance = 5000) to accomplish this. Here is what I run:
options(ChIPseeker.downstreamDistance = 5000) peakAnno <- annotatePeak("test_chr3_regions.bed", level="gene", sameStrand=FALSE, ignoreDownstream=FALSE, ignoreUpstream=FALSE, assignGenomicAnnotation=TRUE, addFlankGeneInfo=TRUE, overlap="all", flankDistance = 10000, genomicAnnotationPriority = c("Promoter", "Intron", "5UTR", "3UTR", "Exon", "Downstream", "Intergenic"), tssRegion=c(-10000, 0),TxDb=test_txdb, verbose=TRUE)
Here is the output: seqnames start end width strand annotation geneChr geneStart geneEnd 1 LALB_chr_3 2627152 2628080 929 Intron (LALB_04121-RA/LALB_04121, intron 3 of 5) 1 2623697 2633465 2 LALB_chr_3 2659533 2660013 481 Distal Intergenic 1 2660123 2661437 3 LALB_chr_3 2664363 2666431 2069 * Promoter (2-3kb) 1 2660123 2661437 geneLength geneStrand geneId distanceToTSS flank_geneIds flank_gene_distances 1 9769 2 LALB_04121 5385 LALB_04121 0 2 1315 2 LALB_04122 1424 LALB_04122 1424 3 1315 2 LALB_04122 -2926 LALB_04122 -2926
The second region is annotated as "Distal Intergenic", but it is only 110bp downstream from the gene LALB_04122. Even the default downstream distance (300, I think) should be greater than 110bp, so the options(ChIPseeker.downstreamDistance = 5000) should not matter here, although I do want to include regions that are within 5kb.
Happy to send files if needed or answer any other questions. Thank you!