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User: madsheilskov

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Posts by madsheilskov

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Get the genomic coordinates for the coding sequence (CDS) of a gene
... 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 2.4 years ago by madsheilskov • 0
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Get the genomic coordinates for the coding sequence (CDS) of a gene
... 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 ...
genomicfeatures txdb.hsapiens.ucsc.hg19.knowngene cds written 2.4 years ago by madsheilskov • 0
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Comment: C: How to find the amino acid codons corresponding to a subset of a range of genomi
... 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 3.2 years ago by madsheilskov • 0
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Comment: C: How to find the amino acid codons corresponding to a subset of a range of genomi
... 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) ? ...
written 3.2 years ago by madsheilskov • 0
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Comment: C: How to find the amino acid codons corresponding to a subset of a range of genomi
... 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 3.2 years ago by madsheilskov • 0
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Comment: C: How to find the amino acid codons corresponding to a subset of a range of genomi
... 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 ?   ...
written 3.2 years ago by madsheilskov • 0
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Comment: C: How to find the amino acid codons corresponding to a subset of a range of genomi
... 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 3.2 years ago by madsheilskov • 0
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How to find the amino acid codons corresponding to a subset of a range of genomic positions
...   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 ...
genomicfeatures genomicranges overlap cds written 3.2 years ago by madsheilskov • 0 • updated 3.2 years ago by Michael Lawrence ♦ 10k
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How to find the amino acid codons corresponding to a subset of a range of genomic positions
...   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 ...
genomicfeatures genomicranges overlap cds written 3.2 years ago by madsheilskov • 0
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Comment: C: How to find the amino acid codon corresponding to a translated genomic position
... 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 3.2 years ago by madsheilskov • 0

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