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BIMSBbioinfo
Site upstream of transcription start site annotated as intronic
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:
chr12 3906815 3908547 ENSMUST00000172913 0 + 3906815 3908265 0 3 68,138,295, 0,790,1437,
Site for annotation (chr12:3905814):
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")
as.data.frame(gr)
seqnames start end width strand
chr12 3905814 3905814 1 *
Annotate:
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 1
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
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
Thank you, something must have been changed in GenomicRanges that causes this.
On Mon, Jan 31, 2022 at 5:28 PM Mike Lee @.***> wrote:
Heya @pkothiyal https://github.com/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
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