User: Harris A. Jaffee

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Posts by Harris A. Jaffee

<prev • 58 results • page 1 of 6 • next >
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Answer: A: mismatch nb in Biostrings
... First, see ?`lowlevel-matching`, and if you are really adventurous, the function nedit_at() in Biostrings/src/lowlevel_matching.c. The degree to which your pattern and subjects disagree, in a sense dictated by your with.indels=FALSE and fixed=TRUE arguments, is determined first, although actually o ...
written 3.4 years ago by Harris A. Jaffee590
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Answer: A: How to do a Vlookup-type function using a value range
... If X and Y are your data frames, the rows you want are given by library(IRanges) nearest(IRanges(X[,"Position"], width=1), IRanges(start=Y[,"Start"], end=Y[,"Stop"])) On May 6, 2014, at 3:34 PM, Elena Sorokin wrote: > I have two data frames as input: > >> small Pos ...
written 3.6 years ago by Harris A. Jaffee590
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Answer: A: What is the easiest way to make the GC content and length matrix for package cqn
... I would like to know the answer! This is all I have. > width(tr_by_gene) IntegerList of length 25529 [["1"]] 6694 [["10"]] 9969 [["100"]] 32214 [["1000"]] 226516 [["10000"]] 355050 343564 343866 355040 343554 343856 [["100008586"]] 187588 6118 6109 [["100008587"]] 156 156 156 156 156 156 156 15 ...
written 3.6 years ago by Harris A. Jaffee590
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Comment: C: get promoter regions (bed format) of genes hg19
... Thanks, Val, for the details. Now I have what is either a shameless plug or a request for explanation. matchGenes() in _bumphunter_ is similar, although definitely not the same. I am not sure how to translate between the results, except to note that matchGenes uses nearest() with either select="a ...
written 3.8 years ago by Harris A. Jaffee590
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Comment: C: rhdf5 segfault
... On Dec 23, 2013, at 10:56 PM, Ben Bolstad wrote: > You might try changing your stack size limits in your shell, before launching R. e.g. > > ulimit -s unlimited I don?t think that is possible, at least as you put it. The soft limit tends to be smaller than the hard limit and is the onl ...
written 3.9 years ago by Harris A. Jaffee590
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Answer: A: Getting first or last hit from a Hits object
... I needed essentially your "last_hits" for bumphunter:::fuzzy.match2 In your notation, it comes out: last_hits_rows <- cumsum(rle(queryHits(all_hits))$lengths) last_hits <- all_hits[last_hits_rows,] Having expended that effort, you could do first_hits_rows <- c(1, ...
written 4.1 years ago by Harris A. Jaffee590
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Comment: C: writeFastq to gzip compressed files
... I believe gzfile only applies when reading. With gzcon, you may have to flush or close the connection (not sure which one - I think your fout2), or your whole session, to get the file written. On Sep 25, 2013, at 4:07 PM, Marcus Davy wrote: > Thanks for the responses, Martin I will give your ...
written 4.2 years ago by Harris A. Jaffee590
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Comment: C: bumphunter::matchGenes and all=TRUE
... Thank you again for the very precise bug report and your data (off list). The annotation handlers for the 10000-nearest-transcript chunks were not being sent the user's value of 'all', so it defaulted to FALSE. Having fixed that, I found out that these handlers also needed a 'queries' and 'Tx' argu ...
written 4.3 years ago by Harris A. Jaffee590
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Comment: C: bumphunter::matchGenes and all=TRUE
... Anne, Can you run it with 'verbose=TRUE'? Also, tell us what your mc.cores value is (This will also appear in the verbose output.)? If it's >1, please try 'mc.cores=1' to see if that makes any difference. On Jul 26, 2013, at 9:45 AM, Kasper Daniel Hansen wrote: > This sounds weird and it ...
written 4.3 years ago by Harris A. Jaffee590
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Comment: C: Trimming of partial adaptor sequences
... On Jul 24, 2013, at 12:26 PM, Taylor, Sean D wrote: > Hi Harris, > > No you are right, I will mostly do 3' trimming. But for my test data it just seemed more convenient to test using Lpattern and I assumed (correctly I hope) that all the same things apply to Rpattern so long as you keep y ...
written 4.3 years ago by Harris A. Jaffee590

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