User: yao.h.1988

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yao.h.19880
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Posts by yao.h.1988

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Comment: C: Is that an efficient way to find the overlapped , upstream and downstream genes
... Thanks, it is all my fault. It works now! ...
written 3.6 years ago by yao.h.19880
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Comment: C: Is that an efficient way to find the overlapped , upstream and downstream genes
...   Many thank, this seems like an undocumented feature. Another question is about how to pass argument to findOverlaps in my own function, I wrote a code like that, but not work range_overlap <- function(query, subject, FUN, ...) { hits <- findOverlaps(query, subject, ...) res <- FUN( ...
written 3.6 years ago by yao.h.19880
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Comment: C: Is that an efficient way to find the overlapped , upstream and downstream genes
... Thanks for your quick reply to remind me the follow() and precede() function. But I think the hardest part to find overlapped gene in the grange itself thus my code just want to fix the overlapped gene first.  I test your code , and also the findOverlaps is wrong, see that: test <- GRanges(seq ...
written 3.6 years ago by yao.h.19880
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Is that an efficient way to find the overlapped , upstream and downstream genes for a bunch of genes
... I do have a bunch of genes ( nearly ~50000)  from the whole genome, which read in genomic ranges I just wondering is there an efficient way to find overlapped, upstream and downstream genes for each gene in the granges For example, assuming all_genes_gr is a ~50000 genes genomic range, the result ...
genomicranges findoverlaps geneoverlap written 3.6 years ago by yao.h.19880 • updated 3.6 years ago by Michael Lawrence11k

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