search for: bsgenom

...ious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped bksl>S4method{enrichmentCalc}{GenomeData, BSgenome}(rs, organism, seqLen=NULL, do.warn=FALSE) <unescaped bksl>S4method{enrichmentCalc}{GRanges, BSgenome}(rs, organism, seqLen=NULL) Functions with \usage entries need to have the appro...

...ious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped bksl>S4method{enrichmentCalc}{GenomeData, BSgenome}(rs, organism, seqLen=NULL, do.warn=FALSE) <unescaped bksl>S4method{enrichmentCalc}{GRanges, BSgenome}(rs, organism, seqLen=NULL) Functions with \usage entries need to have the appro...

Hi, I was installing hundreds of packages on a machine with a single call to install.packages() and after a long time the call to install.packages() finally returned with the following warnings and errors: Warning messages: 1: packages ?hgu133aprobe?, ?hgu95av2.db?, ?BSgenome.Celegans.UCSC.ce2?, ?BSgenome.Mmusculus.UCSC.mm10?, ?BSgenome.Dmelanogaster.UCSC.dm3.masked?, ?BSgenome.Hsapiens.UCSC.hg18.masked?, ?BSgenome.Hsapiens.UCSC.hg19.masked?, ?BSgenome.Mmusculus.UCSC.mm9.masked?, ?BSgenome.Scerevisiae.UCSC.sacCer2?, ?BSgenome.Hsapiens.NCBI.GRCh38?, ?BSgenome.Rno...

I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... }) setMethod("enrichmentCalc", c("GenomeData", "BSgenome"), function(rs, organism, seqLen=NULL, do.warn=FALSE) { ... ... ... }) setMethod("enri...

Over the last several days, I've been working hard to get all of the Fedora R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). With the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and R-rtracklayer, I believe everything is built and updated to the latest versions. And of those packages, they're all ready to go when Fedora infrastructure is working reliably again (the great datacenter migration has started and I can no longer git push). I'll als...

...how to use "loop" to make the process automatic and fast? When compute each sample, the script type in R almost the same, just the input and output file's name is changed(chr1 change to chr2, chr3,chr4...). The first sample's script like this: >chr1=MEDIPS.readAlignedSeqences(BSgenome="hg19", file="chr1",numrows= ) >chr1=MEDIPS.genomeVector(data=chr1, bin_size=50,extend=250) ... ... >write.table(frameschr1.frame500.step250, file="frames.chr1.meth.txt", sep="\T", quote=F, col.names=T, row.names=F) The second sample's script like...

...test if there are coding sequences or exons in hg19 which match a string of 100bp "D" i.e. [A,G or T]. However I'm getting a strange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome") library("Biostrings") library("BSgenome.Hsapiens.UCSC.hg19") library("biomaRt") library("GenomicFeatures") #extract the alignments which match real genes #(add this onto stefans script … req to buid the gr object using the regions from the BSgenom...

...ht into the above problem would be highly appreciated. > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg18_1.3.19 BSgenome_1.28.0 [3] methylPipe_0.99.0 Rsamtools_1.12.3 [5] Biostrings_2.28.0 GenomicRanges_1.12.4 [7] IRanges_1.18.1 GOstats_2.26.0 [9] RSQLite_0.11.4 DBI_0.2-7 [11] graph_1.38.2...

..." would seem more appropriate. - But more importantly, is repos = NULL really supported for update.packages? I wonder where I need to place the local files for this to work. I tried to put them in the current working directory but that didn't work: > packageVersion("BSgenome") [1] ?1.27.1? > dir() [1] "BSgenome_2.0.0.tar.gz" > update.packages(repos=NULL) This description of the 'repos' arg looks more like a copy/paste from the man page for install.packages that needed some edit. - Another copy/paste is the \exam...

Hi, I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Adagenet converts the DNA sequence into retaining only retaining the polymorphic sites and then calcuates Fst.. but is there any other way to do this? I mean analyse the DNA sequence as it is.. and calculate the statistics? Thanks! [[alternative HTML version deleted]]

On Tue, 9 Jun 2020 at 04:42, Tom Callaway <tcallawa at redhat.com> wrote: > > Over the last several days, I've been working hard to get all of the Fedora > R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). With > the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and > R-rtracklayer, I believe everything is built and updated to the latest > versions. And of those packages, they're all ready to go when Fedora > infrastructure is working reliably again (the great datacenter migration > has started and I can no longer git...

On Tuesday, 9 June 2020 03.40.52 WEST Tom Callaway wrote: > Over the last several days, I've been working hard to get all of the Fedora > R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). With > the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and > R-rtracklayer, I believe everything is built and updated to the latest > versions. And of those packages, they're all ready to go when Fedora > infrastructure is working reliably again (the great datacenter migration > has started and I can no longer git...

...affyio * R-ALL * R-AnnotationDbi * R-ape * R-argon2 * R-ascii * R-askpass * R-assertthat * R-AUC * R-backports * R-base64enc * R-Bessel * R-BH * R-biglm * R-bindr * R-bindrcpp * R-Biobase * R-BiocGenerics * R-BiocParallel * R-biomaRt * R-Biostrings * R-bit * R-bit64 * R-bitops * R-blob * R-brew * R-BSgenome * R-BSgenome.Celegans.UCSC.ce2 * R-BufferedMatrix * R-BufferedMatrixMethods * R-Cairo * R-callr * R-car * R-caTools * R-cellranger * R-chron * R-cli * R-cliapp * R-clipr * R-clisymbols * R-coda * R-colorspace * R-combinat * R-commonmark * R-corpus * R-crayon * R-curl * R-data.table * R-date * R-DB...

Hello everyone. There is a new competition, outlined on the blog dataists<http://www.dataists.com/2010/10/using-data-tools-to-find-data-tools-the-yo-dawg-of-data-hacking/>, inviting us to analyse statistics of the use of R packages (collected from 52 R users), to create a R-package suggestion engine for ourselves. Since I noticed several bloggers already wrote about it (as I have detailed

...t; wrote: > On Tuesday, 9 June 2020 03.40.52 WEST Tom Callaway wrote: > > Over the last several days, I've been working hard to get all of the > Fedora > > R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). > With > > the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and > > R-rtracklayer, I believe everything is built and updated to the latest > > versions. And of those packages, they're all ready to go when Fedora > > infrastructure is working reliably again (the great datacenter migration > > has started and...

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

Based on some testing it seems to me that if I have a package with a dataset in /data a Sweave vignette in inst/doc (but no associated pdf file) the vignette loads the data in /data through data(dataset) and I do a R CMD build R will try to build the pdf version of the vignette, but will be unable to find the dataset in data because the package is not yet installed. However, if I do

...dential. Any use...{{dropped:8}} --Forwarded Message Attachment-- From: croosen at mango-solutions.com To: bluejay948 at gmail.com; r-help at r-project.org Date: Mon, 23 Aug 2010 13:20:01 +0100 Subject: Re: [R] DNA sequence Fst Hi, Take a look at the Bioconductor packages, particularly "BSgenome". If that isn't specific enough, you might want to try the Bioconductor mailing list rather than "R-help". http://www.bioconductor.org/packages/release/bioc/html/BSgenome.html bioconductor at stat.math.ethz.ch Best regards, Charlie Roosen Mango Solutions -----Origi...