User: jdavison

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jdavison10
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New User
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United States
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1 year, 9 months ago
Joined:
2 years, 12 months ago
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j*******@fhcrc.org

Posts by jdavison

<prev • 6 results • page 1 of 1 • next >
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Error using goseq function in bioconductor pkg goseq
... Using pkg goseq for the first time; I get this error: > pwf = nullp(genes, 'hg19', 'Gene Symbol', bias.data=df$len) Warning message: In pcls(G) : initial point very close to some inequality constraints > GO.wall = goseq(pwf, 'hg19', 'Gene Symbol') Fetching GO annotations... Error in if (cor ...
goseq written 21 months ago by jdavison10 • updated 21 months ago by Gordon Smyth32k
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Course material from a previous event is not available
... I see that a recent event's material page has a link to pick up the course material, but activating the link returns Access Forbidden.  For example http://bioconductor.org/help/course-materials/2015/SeattleApr2015/ has such a link http://bioconductor.org/help/course-materials/2015/SeattleApr2015/U ...
software error course-material download written 2.6 years ago by jdavison10 • updated 2.6 years ago by Dan Tenenbaum ♦♦ 8.2k
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Answer: A: Affect ShortRead readAligned behavior with ScanBamParam's reverseComplement para
... Sweet, thanks.  And I see you have videos, excellent! http://bioconductor.org/packages/release/bioc/html/GenomicAlignments.html   ...
written 2.9 years ago by jdavison10
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Comment: A: Affect ShortRead readAligned behavior with ScanBamParam's reverseComplement para
... Oops, I forgot to note b = readAligned('my.bam', type='BAM') strand(b) [1] - Levels: + - *   Also, I can get what I want with e.g. bsr = sread(b) ndx = strand(b)=='-' & !is.na(strand(b)) bsr[ndx] = reverseComplement(bsr[ndx])     ...
written 2.9 years ago by jdavison10
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Affect ShortRead readAligned behavior with ScanBamParam's reverseComplement parameter
... Hi, I thought one can affect how ShortRead's readAligned function handles reverse strand BAM reads: to reverse complement them, or not, with the ScanBamParam reverseComplement.  I'm not able to do that, can you set me straight?  Thank you, see the code below. library(ShortRead) b = readAligned(' ...
shortread readaligned reversecomplement scanbamparam written 2.9 years ago by jdavison10
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Comparing AAStrings using identical() instead of ==
... Hi, I made a mistake using identical() to compare 2 AAStrings, as in  identical(AAString('A'), AAString('Z')) which returns TRUE.  That seems to compare lengths.  It took me a while to see I was not getting the result I expected and to learn the correct comparison operator is '=='.  Maybe I should ...
biostrings identical aastring == written 3.0 years ago by jdavison10 • updated 2.9 years ago by Hervé Pagès ♦♦ 13k

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