User: madsheilskov
madsheilskov • 0
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Posts by madsheilskov
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... Yes would be nice with a more streamlined approach as you suggest. Based on your suggestion I ended up doing:
tx_id <- select(Homo.sapiens, keys="APC",columns='TXNAME',keytype="SYMBOL")
cds <- cds(txdb, columns=c("TXNAME","EXONRANK"), vals=list(tx_name=tx_id$TXNAME))
cds_grl <- multisp ...
written 2.8 years ago by
madsheilskov • 0
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... I am relatively new to Bioconductor, and am strugling to find the genome coordinates to a few genes, say for instance "APC". I believe I managed to obtain the transcripts associated with the gene:
library(GenomicFeatures)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(Homo.sapiens)
txdb ...
written 2.8 years ago by
madsheilskov • 0
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... Do you mean (following the ideas above):
grl <- pintersect(tr_hits, tx_hits, drop.nohit.ranges=TRUE )
Here tr_hits and tx_hits are output from findOverlaps() as suggested. Then,
grl_tx <- pmapToTranscripts(unlist(grl), cds[togroup(grl)])
does not work since cds[togroup(grl)] only subsets ...
written 3.5 years ago by
madsheilskov • 0
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... This will not work as pmapToTranscripts() can not take two GrangesLists, namely the one from my pintersect() and the other being cds transcripts from cdsBy().
Perhaps I should not use cdsBy() here (that would intuitively make sense though) ?
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written 3.5 years ago by
madsheilskov • 0
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... Yet, maybe I should not have used unlist() as I now more ranges than the initial 249 list elements since some of my regions ranges overlaps multiple exons. Hence I loose the connection to my query (the ranges) and cannot use pmapToTranscript().
So in the end, I seem to be stucked anyway ?
I us ...
written 3.5 years ago by
madsheilskov • 0
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... Smart, and unlist() afterwards gets you a nice GRanges object. Anyway, do you extract/access individual elements of a GRangeList object; would it be something along lapply perhaps ?
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written 3.5 years ago by
madsheilskov • 0
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... I get the idea, but is stucked after pintersect(). This returns a GRangesList object with the coordinates of the overlaps with transcritps exons and includes a boolean hit mcols. How do I subset this object's TRUE values in order to get the genomic positions (of cds transcripts) with overlap to my r ...
written 3.5 years ago by
madsheilskov • 0
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Recently I asked how one - if given some genomic positions as a GRanges object - could find the amino acid codons that corresponded to these positions (if in a coding exon): https://support.bioconductor.org/p/75497/#75578 . Got a nice solution from the site.
I now find myself in a similar but so ...
written 3.5 years ago by
madsheilskov • 0
• updated
3.5 years ago by
Michael Lawrence ♦ 11k
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Recently I asked how one - if given some genomic positions as a GRanges object - could find the amino acid codons that corresponded to these positions (if in a coding exon): https://support.bioconductor.org/p/75497/#75578 . Got a nice solution from the site.
I now find myself in a similar but so ...
written 3.5 years ago by
madsheilskov • 0
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... Sure - thanks for the comments (many of the Ranges methods are still somewhat new to me and I need to get used using them).
...
written 3.6 years ago by
madsheilskov • 0
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