User: Ivan Gregoretti

gravatar for Ivan Gregoretti
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Posts by Ivan Gregoretti

<prev • 31 results • page 1 of 4 • next >
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Comment: C: ShortReadQ and conversion of quality scores to characters
... Thank you. Ivan On Fri, Jul 11, 2014 at 3:45 PM, Martin Morgan wrote: > On 07/11/2014 09:48 AM, Ivan Gregoretti wrote: >> >> Hello everyone, >> >> Could somebody show how to convert ShortReadQ qualities to characters? >> >> >> A little detail: >& ...
written 3.4 years ago by Ivan Gregoretti310
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ShortReadQ and conversion of quality scores to characters
... Hello everyone, Could somebody show how to convert ShortReadQ qualities to characters? A little detail: For instance, I can load into memory a ShortReadQ instance, A <- readFastq('file.fq.gz') and then I can convert to character either the ID lines or the sequences, as.character(id(A)) as. ...
convert written 3.4 years ago by Ivan Gregoretti310 • updated 3.4 years ago by Martin Morgan ♦♦ 21k
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Answer: A: trying to get TeX or LaTeX for R 3.0.3
... Hello judyh, I think that R is trying to tell you that you should install Tex and/or LaTeX in your system and then compile R. That is how I compile and install my R development branchs in Linux. It may be the same for your operating system. Cheers, Ivan Ivan Gregoretti, PhD Bioinformatics ...
written 3.7 years ago by Ivan Gregoretti310
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Comment: C: fasta biostrings bioconductor
... Hello guest with no name, Have you tried something simple? library(ShortRead) mysequences <- readFasta('FileName.fa') Cheers, Ivan Ivan Gregoretti, PhD Bioinformatics On Fri, Mar 28, 2014 at 12:56 PM, Martin Morgan wrote: > On 03/28/2014 09:43 AM, DNAStringSet Error Biostrings in R ...
written 3.7 years ago by Ivan Gregoretti310
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Comment: C: XCMS for LC-MS
... Hello Bashar, I am unfamiliar to LC-MS with R but a common problem is trying to load in memory a vector that is too big for the hardware or software that you have. To help people help you, I suggest that you execute sessionInfo() at the R prompt and copy/paste that information so that we can at le ...
written 4.0 years ago by Ivan Gregoretti310
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Comment: C: ShortReadQ constructor
... Hi Marcus, Actually, I originally tried using the method (if it existed) to update the ids but got the error that you show above. By the way, going through my records I found that indeed I had a typo. I meant to write ShortReadQ() but I wrote ShortRead(). No wonder it complained about not having a ...
written 4.2 years ago by Ivan Gregoretti310
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Comment: C: ShortReadQ constructor
... The renew() looks really handy. The direct use of the constructor is something that I tried but failed to me. I probably had one of those invisible typos. Thank you. Ivan Ivan Gregoretti, PhD Bioinformatics Cell Signaling Technology, Inc 3 Trask Lane Danvers, MA 01923. USA. Phone +1-978-867-2429 ...
written 4.2 years ago by Ivan Gregoretti310
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Comment: C: ShortReadQ constructor
... Hello Martin, Great. So, srq1 <- ShortReadQ(DNAStringSet(c("ACGT", "GGGGACT")), FastqQuality(c("HHHH", "HHHHHHH")), BStringSet(c("read1", "read2"))) gets me what I wanted. Now I have a part two to my question: How do I modify srq1's id? For instance, id(srq1) produces > id(srq1) A BStr ...
written 4.2 years ago by Ivan Gregoretti310
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ShortReadQ constructor
... Hello, Could somebody show an example of constructing a ShortReadQ object instance? I can't find an example in the documentation. For example, lets say that I have two records with the following ids, sequences, and Phred qualities c("read1", "read2") c("ACGT", "GGGGACT") c("HHHH", "HHHHHHH") Ho ...
written 4.2 years ago by Ivan Gregoretti310 • updated 4.2 years ago by Martin Morgan ♦♦ 21k
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Answer: A: installation packages
... Please try again but this time do it as root instead of a regular user. Its a common mistake. Ivan Ivan Gregoretti, PhD Bioinformatics On Fri, Sep 13, 2013 at 10:21 AM, fran vino wrote: > Dear Bioconductor list, > > I installed R on UBUNTU, but now how can I install the packages i ...
written 4.3 years ago by Ivan Gregoretti310

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