AstrobioMike
commented
2 years ago Heya @pkothiyal and devs,
I happened to peek at this too, and just because of the older version of R where I tested, version 1.16.0 of genomation was installed, and this didn't happen in that version (in case it helps track down whatever is going on):
library(genomation)
packageVersion("genomation") # 1.16.0
library(GenomicRanges)
packageVersion("GenomicRanges") # 1.36.1
bed <- c("chr12", 3906815, 3908547, "ENSMUST00000172913", 0, "+", 3906815, 3908265, 0, 3, "68,138,295,", "0,790,1437,")
bed_df <- t(data.frame(bed))
write.table(bed_df, "mm10.bed", sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
df <- data.frame (chr = c("chr12"),
start = c(3905814),
end = c(3905814)
)
gr <- makeGRangesFromDataFrame(df, keep.extra.columns = FALSE,
start.field = "start",
end.field = "end")
gene.obj <- readTranscriptFeatures("mm10.bed", up.flank = 1000, down.flank = 1000, remove.unusual = TRUE, unique.prom = TRUE)
annRes <- annotateWithGeneParts(gr, gene.obj)
cbind(getAssociationWithTSS(annRes), as.data.frame(getMembers(annRes)))
# target.row dist.to.feature feature.name feature.strand prom exon intron
# 1 -1002 ENSMUST00000172913 + 0 0 0
sessionInfo()
# R version 3.6.3 (2020-02-29)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS 10.16
#
# Matrix products: default
# LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
#
# locale:
# [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#
# attached base packages:
# [1] parallel stats4 grid stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] GenomicRanges_1.36.1 GenomeInfoDb_1.20.0 IRanges_2.18.3 S4Vectors_0.22.1 BiocGenerics_0.30.0 genomation_1.16.0
#
# loaded via a namespace (and not attached):
# [1] Rcpp_1.0.8 lattice_0.20-45 Rsamtools_2.0.3 Biostrings_2.52.0
# [5] assertthat_0.2.1 utf8_1.2.2 gridBase_0.4-7 R6_2.5.1
# [9] plyr_1.8.6 ggplot2_3.3.5 pillar_1.6.5 zlibbioc_1.30.0
# [13] rlang_1.0.0 rstudioapi_0.13 data.table_1.14.2 Matrix_1.2-18
# [17] BiocParallel_1.18.1 readr_2.1.1 stringr_1.4.0 RCurl_1.98-1.5
# [21] bit_4.0.4 munsell_0.5.0 DelayedArray_0.10.0 compiler_3.6.3
# [25] rtracklayer_1.44.4 pkgconfig_2.0.3 tidyselect_1.1.1 SummarizedExperiment_1.14.1
# [29] tibble_3.1.6 GenomeInfoDbData_1.2.1 matrixStats_0.61.0 XML_3.99-0.3
# [33] fansi_1.0.2 withr_2.4.3 crayon_1.4.2 dplyr_1.0.7
# [37] tzdb_0.2.0 GenomicAlignments_1.20.1 bitops_1.0-7 gtable_0.3.0
# [41] lifecycle_1.0.1 DBI_1.1.2 magrittr_2.0.2 scales_1.1.1
# [45] KernSmooth_2.23-20 cli_3.1.1 stringi_1.7.6 impute_1.58.0
# [49] vroom_1.5.7 XVector_0.24.0 reshape2_1.4.4 ellipsis_0.3.2
# [53] generics_0.1.1 vctrs_0.3.8 tools_3.6.3 bit64_4.0.5
# [57] BSgenome_1.52.0 Biobase_2.44.0 glue_1.6.1 seqPattern_1.16.0
# [61] purrr_0.3.4 hms_1.1.1 plotrix_3.8-2 colorspace_2.0-2
# [65] BiocManager_1.30.16 
al2na
Hi, I tried annotating a few sites with annotateWithGeneParts and I'm getting an intron annotation even though the site is upstream of transcription start site. Here's an example:
BED12 entry for the associated transcript:
Site for annotation (chr12:3905814):
Annotate:
As seen above, the site is annotated in the intron of the transcript even though it is 1002 bases upstream of the transcription start site. The promoter flank is set at 1,000 so I understand it not being mapped to promoter but should it be intergenic instead of intronic in this case?
Thanks, Prachi