User: Mike Smith

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Mike Smith1.4k
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Posts by Mike Smith

<prev • 209 results • page 1 of 21 • next >
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Comment: C: Extracting all possible annotations between two genomic coordinates
... Yes, that should do it.  You can also do this using the standard useMart() function, and specifying one of the ensembl archives as the host.  This is a little more flexible than useEnsembl() So for GRCh37 you would use: useMart(biomart = 'ENSEMBL_MART_ENSEMBL', dataset="hsapiens_gene_ense ...
written 7 hours ago by Mike Smith1.4k
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Comment: C: how to extract part of the DNA sequences from a DNAstringset
... Do you really want to remove the entries that start with 0?  If you want to do that you could this: hits.frame <- hits.frame[ which(hits.frame$start > 0) , ] This finds all the rows where the start value greater than 0, and only returns those.  Perhaps you would rather change the 0 entries ...
written 8 hours ago by Mike Smith1.4k
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Answer: A: Extracting all possible annotations between two genomic coordinates
... You could try using the biomaRt package to query the various ensembl databases. For example, to find genes in a region, and their GC content, you can do something like this: library(biomaRt) genes_mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") getBM(mart = mart, attr ...
written 14 hours ago by Mike Smith1.4k
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Answer: A: how to extract part of the DNA sequences from a DNAstringset
... How about something like this?  First we'll set up an example with 3 DNA sequences, and we're going to look for the pattern TACG in each of them, just like you've already done. dna_initial <- DNAStringSet(c("ACGTACGGACGT", "GTACGTACGGAC", ...
written 15 hours ago by Mike Smith1.4k
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Answer: A: biomaRt's uniprot_swissprot and uniprot_sptrembl attributes
... Rather than a discussion on keeping multiple IDs in sync across multiple databases, which is something that has proved challenging for as long as I've been in this field, for now I'll offer a possible solution based on gene names, which I find to be slightly more reliable between sources. Suffice to ...
written 15 days ago by Mike Smith1.4k
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Answer: A: Error in getBM of biomaRt package
... I'm pretty certain this error is related to issues with the Ensembl biomart server, but I'm currently not seeing this when I run your code, so maybe it's been fixed already.  If you experience it again, you can always try one of the Ensembl mirror sites to see if they're working, like this: mart ...
written 18 days ago by Mike Smith1.4k
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Answer: A: Splitting a GRanges object into List of GRange objects by position.
... How about this: split(gr, as.factor(gr)) > GRangesList object of length 2: $chr1:50-100:+ GRanges object with 2 ranges and 1 metadata column: seqnames ranges strand | scores <Rle> <IRanges> <Rle> | <numeric> [1] chr1 [50, 100] + | ...
written 21 days ago by Mike Smith1.4k
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Answer: A: Bug in rhdf5::h5write?
... I think this is because h5write isn't registered as an S3method.  When you haven't attached rhdf5 using library(), R looks for the appropriate method in the environment, and then in the database of registered methods, but it won't find it in either and fails.  Once you've run library() the h5write.d ...
written 21 days ago by Mike Smith1.4k
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Answer: A: do.call error "second argument must be a list" with GRanges object
... How about this? ​matches <- lapply(grs, match, resGR) reList <- lapply(matches, function(x, res) { x <- na.omit(x) res[x] }, resGR) reList <- as(reList, "GRangesList") The first line takes the input GRangesList, and for each entry finds any matches in your output GRanges object. ...
written 23 days ago by Mike Smith1.4k
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Comment: C: do.call error "second argument must be a list" with GRanges object
... I'm not sure I totally follow what you're trying to do, but does resGR now contain a subset of the ranges in your original GRangesList, but in a different order?  Any you're trying to match them back to the original?  Is it intentional that you have one fewer range in resGR? ...
written 23 days ago by Mike Smith1.4k

Latest awards to Mike Smith

Scholar 19 hours ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 18 days ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
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Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2 color coding
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more g
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
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Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2 color coding
Scholar 10 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Scholar 10 months ago, created an answer that has been accepted. For A: Retrieve SNP flanking sequences in biomaRt
Scholar 10 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Scholar 10 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more g
Scholar 10 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
Scholar 11 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more g
Scholar 12 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
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Scholar 12 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
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