Re: [Bioc-devel] Combining Ordinary List of GRanges Optimisation

2013-01-06 Thread Dario Strbenac
Are you asking if you can rewrite your code to work faster, or are you asking if the BioC devs need to improve the code to be faster? I was suggesting that maybe the c function for GRanges could be optimised. Another would be manually splitting each GRanges objects into its components:

[Bioc-devel] oligonucleotideFrequency Performance Enhancement

2013-02-05 Thread Dario Strbenac
is specified. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman

[Bioc-devel] maPlot Fold Change

2013-05-22 Thread Dario Strbenac
Hello, In the documentation of maPlot, it doesn't state that the fold change is calculated as y / x. It would be good to have it stated, since x / y is just as valid. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

[Bioc-devel] rtracklayer import Error

2013-07-15 Thread Dario Strbenac
stats4_3.0.1 tools_3.0.1 XML_3.98-1.1 [9] zlibbioc_1.6.0 -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch

[Bioc-devel] Parsing Error for UCSC Table

2013-07-15 Thread Dario Strbenac
-- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] rtracklayer Export BED itemRgb Annotation

2013-07-18 Thread Dario Strbenac
The documentation says that itemRgb must be a character vector of hex color codes, as returned by col2rgb. However, the return value of col2rgb is An integer matrix with three or four rows. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW

[Bioc-devel] Available Columns for GenomicFeatures select

2013-07-22 Thread Dario Strbenac
] EXONNAME EXONCHROM EXONSTRAND EXONSTART EXONENDGENEID TXID [15] EXONRANK TXNAME TXCHROMTXSTRAND TXSTARTTXEND I have the newest GenomicFeatures and R 3.0.1. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050

[Bioc-devel] Return Type of as.table on Hits Object

2013-07-26 Thread Dario Strbenac
?`Hits-class` explains that as.table returns an object of class table, but it's an integer vector. class(peaksToGenes) [1] Hits attr(,package) [1] IRanges class(as.table(t(peaksToGenes))) [1] integer This is in IRanges_1.18.2 -- Dario Strbenac PhD Student

[Bioc-devel] Running Time of readBamGappedAlignmentPairs

2013-07-28 Thread Dario Strbenac
59.00 1939.11 system.time(RNAreads - readBamGappedAlignments(file)) user system elapsed 192.808.12 214.97 -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r

Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs

2013-07-29 Thread Dario Strbenac
:29 PM To: Dario Strbenac Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs Hi Dario, The function was optimized in Bioc-devel. Depending on the number of records in your BAM file (which is more relevant than its size), it should now be between 2x

Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs

2013-08-06 Thread Dario Strbenac
Pagès Cc: Dario Strbenac; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs On 07/31/2013 04:05 PM, Hervé Pagès wrote: Hi Dario, Thanks for providing the file. The file has 55780092 records in it and yes it only contains primary alignments so

[Bioc-devel] GenomicFeatures LoadDb Path

2013-08-08 Thread Dario Strbenac
'loadDb': Error: argument dbType is missing, with no default # Help file says this is optional. genes17 - loadDb(gencode17.db) AnnotationDbi_1.22.6 -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

Re: [Bioc-devel] Parsing Error for UCSC Table

2013-08-10 Thread Dario Strbenac
The cause of this was determined to be a bug in an outdated Apache server. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Heatplus Heatmap Fails for Hidden Dendrogram and Labels

2013-10-13 Thread Dario Strbenac
= 1:18), side = list(Row = 4, Col = 1 Error in mmar[x$labels$Row$side] = x$labels$Row$nrow : invalid subscript type 'list' I use version 2.6.0. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

Re: [Bioc-devel] Heatplus Heatmap Fails for Hidden Dendrogram and Labels

2013-10-14 Thread Dario Strbenac
Thanks. That solves most of the problems. When I resize the plot window of Rstudio to any size, it still gives an error. Can you reproduce this with random data ? Here is an example that creates a large PDF, but still causes the error. values - matrix(rnorm(45*18), nrow = 45) pdf(tmp.pdf,

[Bioc-devel] lumiT VST Normalisation Fails

2013-11-01 Thread Dario Strbenac
the entire PDF manual of the help pages also does not show SampleID described anywhere. I am using lumi 2.14.0. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org

Re: [Bioc-devel] lumiT VST Normalisation Fails

2013-11-02 Thread Dario Strbenac
again, with the necessary columns. It's also missing the number of beads column. From: du4p...@gmail.com du4p...@gmail.com on behalf of Pan Du dupan.m...@gmail.com Sent: Saturday, 2 November 2013 3:31 AM To: Dario Strbenac Cc: bioc-devel@r-project.org Subject: Re

[Bioc-devel] IlluminaID2nuID Incorrectly Uses If Statement

2013-12-01 Thread Dario Strbenac
to an if statement. The arrays are an older type. They use probe IDs like 6450255 not like ILMN_12345. I have another batch of newer arrays. No warning happens for them. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

Re: [Bioc-devel] IlluminaID2nuID Incorrectly Uses If Statement

2013-12-02 Thread Dario Strbenac
getChipInfo(rownames(stage3expression), species = Human) $chipVersion [1] HumanHT12_V3_0_R3_11283641_A HumanWG6_V3_0_R3_11282955_A $species [1] Human $IDType [1] Array_Address_Id Array_Address_Id $chipProbeNumber [1] 48803 $inputProbeNumber [1] 48803 $matchedProbeNumber [1] 48803

[Bioc-devel] EBSeq Documentation of maxround

2014-01-22 Thread Dario Strbenac
Hello, The documentation says : maxroundNumber of iterations. The default value is 5. However, if I call the EBTest function without specifying maxround, it has an error : Error in 1:maxround : 'maxround' is missing -- Dario Strbenac PhD Student

[Bioc-devel] EBSeq C1Mean and C2Mean Values

2014-01-22 Thread Dario Strbenac
nicely into a data frame. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Installing Annotation Packages Matching a Pattern

2014-05-04 Thread Dario Strbenac
guide simply advises Visit the Workflows page and software package list to discover available packages. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org

Re: [Bioc-devel] Installing Annotation Packages Matching a Pattern

2014-05-05 Thread Dario Strbenac
Thanks for this code. I was interested in all of the BSgenome packages, so the results are sufficient for what we want on our group's server. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] deprecating GenomeData and GenomeDataList

2014-05-08 Thread Dario Strbenac
We could simply remove the GDL2GRL function once the GenomeData and GenomeDataList are defunct. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Contradictory Clinical Data in curatedOvarianData

2014-05-20 Thread Dario Strbenac
as days_to_tumor_recurrence, for the first sample ? -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc

Re: [Bioc-devel] edgeR estimateGLMRobustDisp Fails when Called From A Package

2014-06-26 Thread Dario Strbenac
of LargeDataObject from limma is not imported into edgeR. Can you add that one, too ? -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia From: Gordon K Smyth sm...@wehi.edu.au Sent: Friday, 27

Re: [Bioc-devel] edgeR estimateGLMRobustDisp Fails when Called From A Package

2014-06-27 Thread Dario Strbenac
Extends: Class list, from data part Class LargeDataObject, directly Class vector, by class list, distance 2 That's why edgeR needs to know about that class. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

Re: [Bioc-devel] edgeR estimateGLMRobustDisp Fails when Called From A Package

2014-06-27 Thread Dario Strbenac
, and consequently will not find their dependencies unless hacked. From my introductory reading, it seems to be that Imports is preferred over Depends. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

[Bioc-devel] GOHyperGParams Minimum Size

2014-07-10 Thread Dario Strbenac
. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] DESeqDataSetFromMatrix Changes Column Names

2014-08-24 Thread Dario Strbenac
: 2: sampleNames differ between phenoData and protocolData -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo

Re: [Bioc-devel] DESeqDataSetFromMatrix Changes Column Names

2014-08-25 Thread Dario Strbenac
I am using the latest release version. I understand your recommendation about colData and will use it. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r

[Bioc-devel] Documentation Link to S4 Class from Package in Suggests Field

2014-09-22 Thread Dario Strbenac
a previous question that remains unanswered. https://stat.ethz.ch/pipermail/bioc-devel/2007-March/001001.html -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org

[Bioc-devel] Installing Development Version of Repitools

2014-10-01 Thread Dario Strbenac
? -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Installing Development Version of Repitools

2014-10-01 Thread Dario Strbenac
After properly updating all my packages, there is no problem. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] biovizBase Installation rbind Problem

2014-12-11 Thread Dario Strbenac
for package 'spliceR' * removing '/dskh/nobackup/biostat/Bioconductor/spliceR' * restoring previous '/dskh/nobackup/biostat/Bioconductor/spliceR' -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

Re: [Bioc-devel] IRanges findOverlaps Result Different for Recent Update

2015-01-15 Thread Dario Strbenac
The order of results is not important for the analysis. I have updated the test case with a new expected result. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r

[Bioc-devel] ClassifyR Fails to Build on Windows

2015-01-15 Thread Dario Strbenac
without problems for Linux and Mac OS. Is there a flaw in the development version of BiocParallel ? -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing

Re: [Bioc-devel] ClassifyR Fails to Build on Windows

2015-01-16 Thread Dario Strbenac
using parallelisation ? -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] IRanges findOverlaps Result Different for Recent Update

2015-01-14 Thread Dario Strbenac
soon ? The two sets of intervals to produce this result are anno and probesGR, defined in the tests.R file in the Repitools package. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

Re: [Bioc-devel] ClassifyR Fails to Build on Windows

2015-01-15 Thread Dario Strbenac
which caused a problem, which remains in version 1.11.11. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman

[Bioc-devel] GEOquery Warnings When Reading SOFT File

2015-02-18 Thread Dario Strbenac
(gastricChina) gives an empty result Experiment data Experimenter name: Laboratory: Contact information: Title: URL: PMIDs: No abstract available. whereas some of the fields are filled in on the webpage. -- Dario Strbenac PhD Student

Re: [Bioc-devel] new package: canceR

2015-03-26 Thread Dario Strbenac
) and clinical data, but I don't see how it could be done with canceR. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman

[Bioc-devel] biocUpgrade Wrongly Infers R Version

2015-04-27 Thread Dario Strbenac
? http://www.bioconductor.org/checkResults/release/bioc-LATEST/ -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman

[Bioc-devel] S4 Method of ExpressionSet Signature Not Found

2015-10-22 Thread Dario Strbenac
ection") for currently available ones. Browse[2]> do.call(selectParams@featureSelection, paramList) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'DMDselection' for signature '"ExpressionSet"' ---

Re: [Bioc-devel] S4 Method of ExpressionSet Signature Not Found

2015-10-22 Thread Dario Strbenac
nature '"ExpressionSet"' It only happens after I use : detach("package:ClassifyR", unload = TRUE) install.packages("ClassifyR/", repos = NULL) library(ClassifyR) because I'm modifying the package code and installing it repeatedly, to f

Re: [Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

2015-11-16 Thread Dario Strbenac
Hello, How does your package differ to importing GSE62944 into R with AnnotationHub http://bioinformatics.oxfordjournals.org/content/31/22/3666.long ? It seems like unnecessary duplication. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW

Re: [Bioc-devel] bplapply Processes Sometimes Stall

2016-01-01 Thread Dario Strbenac
56 I use : R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) with BiocParallel 1.5.12 ------ Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050

Re: [Bioc-devel] bplapply Processes Sometimes Stall

2015-12-29 Thread Dario Strbenac
Good day, The problem is avoided by explicitly using bpstart and bpstop functions. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https

[Bioc-devel] Progress Message Order in bplapply

2015-12-27 Thread Dario Strbenac
= MulticoreParam(workers = 25)) The resulting progress message aren't displayed until the end of the process, whereas before they appeared immediately. I would expect 10 and 20 to appear before 30 did. 30 40 50 10 20 60 70 80 90 100 -- Dario Strbenac PhD

[Bioc-devel] bplapply Processes Sometimes Stall

2015-12-27 Thread Dario Strbenac
es: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] BiocParallel_1.4.3 loaded via a namespace (and not attached): [1] futile.logger_1.4.1 lambda.r_1.1.7 futile.options_1.0.0 ------ Dario Strbe

Re: [Bioc-devel] Pushing updates in the release branch

2016-05-26 Thread Dario Strbenac
becomes the release variety. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] bplapply Processes Sometimes Stall

2016-01-17 Thread Dario Strbenac
Hello, Running the code serially works and running it on an Ubuntu 15.10 server also works. The problem has only been found with Debian 8.2. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

Re: [Bioc-devel] bplapply Processes Sometimes Stall

2016-02-22 Thread Dario Strbenac
3.2.4 version, but without a small example, I don't know how to convince the developers to do that. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing

Re: [Bioc-devel] bplapply Processes Sometimes Stall

2016-01-22 Thread Dario Strbenac
the problem. Now I need to convince the server administrator (who relies on the availability of Debian packages and apt-get) to install R from source on the servers! -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

[Bioc-devel] Strand-Awareness for Restrict Function

2016-02-14 Thread Dario Strbenac
alternative, if the first and last 50 bases are calculated of each chromosome. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch

[Bioc-devel] Efficient Random Sampling of Positions in GRanges

2016-02-16 Thread Dario Strbenac
. The construction of the GRanges object containing every chromosome position is inefficient, as is finding its overlaps with another GRanges object. Could an optimised function for this task be added to GenomicRanges ? -- Dario Strbenac PhD Student University

Re: [Bioc-devel] Efficient Random Sampling of Positions in GRanges

2016-02-18 Thread Dario Strbenac
dataset, and for regions to be possibly chosen on the opposite strand to a masked region, such as when the genome is masked by transcripts for the purpose of choosing intergenic sequences. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050

[Bioc-devel] Package Without a Vignette

2016-03-22 Thread Dario Strbenac
Hello, The newly added Bioconductor package miRNAmeConverter has no vignette, although a vignette is a requirement for Bioconductor packages which are not simply annotation databases. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050

Re: [Bioc-devel] New package submission warning

2016-05-22 Thread Dario Strbenac
one converted their GEO or ArrayExpress dataset into a Bioconductor package, Bioconductor would quickly become cluttered. ------ Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@

[Bioc-devel] getGEO for Private Datasets

2016-05-16 Thread Dario Strbenac
the dataset private until the article is published. Reviewers would also benefit from the convenience. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing

Re: [Bioc-devel] inquiry about possibility of package name change

2016-07-04 Thread Dario Strbenac
to yours. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] edgeR and limma Default Offsets

2017-02-15 Thread Dario Strbenac
Good day, The cpm function in edgeR uses a default offset of 0.25 and voom in limma uses 0.5 (and provides no user modification) to calculate the base 2 logarithm of the counts per million. Might these be made consistent? -- Dario Strbenac University

Re: [Bioc-devel] edgeR and limma Default Offsets

2017-02-16 Thread Dario Strbenac
counts + 0.5)/(lib.size + 1) Basically, the values added to the counts and the library size ignore the library size of each sample in the voom function. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Aus

Re: [Bioc-devel] BStringSet Documentation

2016-09-02 Thread Dario Strbenac
Hello, Actually, I thought that substr unintentionally worked and perhaps they should both produce an error message. Thanks for adding the functionality for strsplit, though! -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

[Bioc-devel] BStringSet Documentation

2016-09-01 Thread Dario Strbenac
split(IDs, " ") : non-character argument I think that both of these functions shouldn't work or both should work, to be consistent. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] String Matching in Parallel

2016-09-04 Thread Dario Strbenac
calling DNAString (it's odd that vmatchPattern - for searching BSgenome objects - requires a DNAString for the pattern, rather than a DNAStringSet) or DNAStringSet ? -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

Re: [Bioc-devel] Why sleuth is not in Bioconductor?

2016-09-14 Thread Dario Strbenac
nction documentation with runnable examples and a vignette. Sleuth isn't currently at the R package quality level necessary for Bioconductor. ------ Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

[Bioc-devel] Repitools Development Version Webpage Gone

2016-08-26 Thread Dario Strbenac
Recently, the overview webpage of the development version of Repitools has vanished. It is still listed in the build report, though. There are also some strange build errors on Linux. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

[Bioc-devel] VCF Intersection Using readVcf Remarkably Slow

2016-09-27 Thread Dario Strbenac
hat is 4 GB in size when compressed. I can't imagine how long that would take. Can the code of readVcf be optimised ? -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Warning when Reading Example VCF

2016-09-27 Thread Dario Strbenac
d user. R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 15.10 VariantAnnotation 1.18.7 ------ Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project

Re: [Bioc-devel] chimera Attempts to Open Non-existent File

2016-11-06 Thread Dario Strbenac
. - Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Subversion Log Stalled

2016-11-10 Thread Dario Strbenac
Good day, The log at http://bioconductor.org/developers/svnlog/ stopped updating two weeks ago. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https

Re: [Bioc-devel] Bioc-devel Digest, Vol 152, Issue 10

2016-11-06 Thread Dario Strbenac
for the file's existence at the beginning of the function. For example, if(file.exists(filename)) # Do fusion file import. else stop("Could not find the specified fusion file.") ------ Dario Strbenac University of Sydney Camperdown NSW 2050

[Bioc-devel] vmatchPattern Returns Out of Bounds Indices

2016-11-16 Thread Dario Strbenac
to their corresponding sequence in 'x' It's rare, but still a problem, nonetheless. > table(unlist(endIndex(primerLocations)) > 75) FALSE TRUE 366225 2 This happens with Biostrings 2.42.0. ------ Dario Strbenac University of Sydney C

[Bioc-devel] Feasibility of Parallel Extraction of Matches with extractAllMatches

2016-11-16 Thread Dario Strbenac
d since it duplicates the functionality of substr? > substr(words, start(matches), end(matches)) [1] "GOAT" "MOAT" NA Also, the expected subsetting fails for MIndex objects. > class(matches) [1] "ByPos_MIndex" > length(matches) [1] 3 > length(matches[1]) [1] 3

Re: [Bioc-devel] vmatchPattern Returns Out of Bounds Indices

2016-11-18 Thread Dario Strbenac
attern() does not support indels yet This is utilising Biostrings 2.42.0 in R 3.3.1. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/m

[Bioc-devel] FlipFlop Ignores Read Strand and Requires Antiquated File Formats

2016-11-01 Thread Dario Strbenac
provide GTF and GFF3 files, which can easily be imported into R with functions provided by rtracklayer. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https

[Bioc-devel] ignoreSelf Option for findOverlaps of GenomicRanges Query

2016-10-26 Thread Dario Strbenac
to be consistent? -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] chimera Attempts to Open Non-existent File

2016-11-02 Thread Dario Strbenac
: Warning message: In file(file, "rt") : cannot open file 'Thu_Nov_3_13-46-27_2016': No such file or directory The section of code where the error occurs seems to be in the .starImport function. ------ Dario Strbenac Univ

Re: [Bioc-devel] NEWS files

2016-10-12 Thread Dario Strbenac
s gigantic. ------ Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] NEWS files

2016-10-12 Thread Dario Strbenac
Good day, I see it, too. There's no problem. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] readGAlignmentPairs Fails if Used Inside mclapply Loop

2016-12-12 Thread Dario Strbenac
cores = 2 and it also resulted in an error. Each of the files has 30 to 40 million mappings, so I wouldn't expect them to be too big. I'll stick to bplapply. ------ Dario Strbenac University of Sydney Camperdown NSW 2050

[Bioc-devel] readGAlignmentPairs Fails if Used Inside mclapply Loop

2016-12-12 Thread Dario Strbenac
IRanges_2.8.1 S4Vectors_0.12.0 BiocGenerics_0.20.0 loaded via a namespace (and not attached): [1] zlibbioc_1.20.0BiocParallel_1.8.1 lattice_0.20-34tools_3.3.2 grid_3.3.2 DBI_0.5-1 Matrix_1.2-7.1 [8] rtracklayer_1.34.1 bitops_1.0-

Re: [Bioc-devel] readGAlignments Lacks strandMode

2017-01-14 Thread Dario Strbenac
Good day, Now I know about invertStrand, I agree that it's best to keep the strandMode only for paired-end data. Indeed, it's an example at the end of the lengthy documentation of GAlignments. -- Dario Strbenac University of Sydney Camperdown NSW 2050

[Bioc-devel] Implementation of vmatchPattern Indels

2016-12-04 Thread Dario Strbenac
of CRISPR genomic screens without leaving the R analysis environment, which is a new use case not existing before. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org

[Bioc-devel] asBam Default Destination

2017-01-06 Thread Dario Strbenac
x "bam" instead of "sam"? -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] GAlignments Sorting Causes C Stack Error

2017-01-08 Thread Dario Strbenac
cs_0.20.0 loaded via a namespace (and not attached): [1] lattice_0.20-34bitops_1.0-6 grid_3.3.2 zlibbioc_1.20.0 Matrix_1.2-7.1 BiocParallel_1.8.1 [7] tools_3.3.2 ------ Dario Strbenac University of Sydney Camperdown NSW 2050

[Bioc-devel] readGAlignments Lacks strandMode

2017-01-05 Thread Dario Strbenac
for readGAlignments and other similar functions in GenomicAlignments. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc

[Bioc-devel] Alternative Hypothesis Specification For edgeR

2017-01-15 Thread Dario Strbenac
Good day, In a future release, could the user be allowed to specify an alternative hypothesis such as the coefficient being positive? DESeq2 provides an altHypothesis parameter for such a purpose. -- Dario Strbenac University of Sydney Camperdown NSW 2050

[Bioc-devel] GRangesList Conversion Fails For Unstranded Sequencing Data

2017-03-14 Thread Dario Strbenac
. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] ShortReadQ Serialisation Slow and Creates Large File

2017-04-26 Thread Dario Strbenac
ved in binary format, the size on disk is 2.0 GB. Is a lot of unnecessary detail saved when the object is serialised? -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.

[Bioc-devel] pairwiseAlignment Improvements

2017-04-28 Thread Dario Strbenac
ocumented in Numeric Summary Methods? Unlike nchar and score, they are not numerical summaries of the data. It'd be nice to see this part of Biostrings thoroughly refactored with more focus on UX. -- Dario Strbenac

[Bioc-devel] Default Coverage Value

2017-07-27 Thread Dario Strbenac
verage(foo, bar, ..., NA.value=-1)?" - Tim Triche, Jr., January 2013. Might this plan be restored (with a default value of 0 for backwards compatibility)? ------ Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

Re: [Bioc-devel] git and public keys

2017-08-22 Thread Dario Strbenac
Good day, Is the private key in a location other than the default SSH key folders? If so, use the ssh-add command to have the SSH agent know about it. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

[Bioc-devel] SplicingGraphs Feature Suggestion

2017-06-22 Thread Dario Strbenac
Hello, It would be convenient if the colour or the width of the edges could be customised to represent whether an edge is equally present in two experimental conditions or the degree to which it is enriched in one of them of an RNA-seq dataset. -- Dario

Re: [Bioc-devel] ExperimentList Contructor Failing

2017-09-12 Thread Dario Strbenac
Good day, Whatever the problem is, it's gone with R Under Development and all packages installed from the development branch of Bioconductor. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

[Bioc-devel] MultiAssayExperiment Subsetting Fails if Column Data Has One Column

2017-09-12 Thread Dario Strbenac
classes) measurementsSet[1, 1, ] other attached packages: [1] S4Vectors_0.15.7BiocGenerics_0.23.1 MultiAssayExperiment_1.3.34 -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

[Bioc-devel] ExperimentList Contructor Failing

2017-09-12 Thread Dario Strbenac
;3.2.3" "0.9-8" Repository rJava "https://cran.rstudio.com/src/contrib; update with biocLite() Error: 1 package(s) out of date The same example works on another computer using Windows operating system. What's the issue with this Linux e

Re: [Bioc-devel] Generate valid SSH keys for the bioc-git server!

2017-08-21 Thread Dario Strbenac
Good day, I filled out the form on Thursday, but can't fetch the repository. $ git fetch upstream Permission denied (publickey). fatal: Could not read from remote repository. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

[Bioc-devel] SnpSet Creation Function Prototype Not Valid R Code

2017-08-23 Thread Dario Strbenac
, object creation using new is discouraged. Perhaps SnpSet could have a proper constructor, like ExpressionSet does? -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing

  1   2   >