[ensembl-dev] an error in biomart regarding chr21

Bogdan Tanasa tanasa at gmail.com
Tue Jul 3 01:49:58 BST 2018


Dear all,

I am writing to ask please for a piece of help regarding biomart and R. I
am using the piece of R code below, that was inspired by the package
StructuralVariantAnnotation :

https://github.com/PapenfussLab/gridss/blob/master/example/somatic-fusion-
gene-candidates.R; to annotate the Structural Variants from DELLY.

However, the coordinates on chr21 are not annotated properly, in the sense
that : shall I input the following coordinates for a breakpoint
"chr21:10813930-10813931", it gives me the gene annotations such as
"SMIM11B,U2AF1L5,LOC102724652,CRYAA,U2AF1,CBS"
I can send you the full code in R, if you wish. Would you please let me
know --- how shall I fix it ? thank you very much !

-- bogdan

##################### the piece of R code that I am using is the following
: ###########################################################

gns <- genes(TxDb.Hsapiens.UCSC.hg38.knownGene)

hits <- as.data.frame(findOverlaps(gr, gns, ignore.strand=TRUE))


hits$SYMBOL <- biomaRt::select(org.Hs.eg.db, gns[hits$subjectHits]$gene_id,
"SYMBOL")$SYMBOL

hits$gene_strand <- as.character(strand(gns[hits$subjectHits]))

hits <- hits %>%
  group_by(queryHits) %>%
  summarise(SYMBOL=paste(SYMBOL, collapse=","), gene_strand=paste0(gene_strand,
collapse=""))
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