search for: snpmatrix

Hi R-help folks, I have been doing some single SNP association work using snpMatrix. This works well, but produces a lot of false positives, because of population structure in my data. I would like to correct the p-values (which snpMatrix gives me) for population structure, possibly using principle component analysis (PCA). My data is complicated, so here's a simple examp...

...20150122.zip in http://sourceforge.net/projects/outmodedbonsai/files/R/ The cairo replacements are just two bundles, windows or OS X - containing replacements for R 2.15.3, 3.0.3 and 3.1.2. You just extract the relevant one for your R version. The windows builds of R packages snpStats x.x.x.8 and snpMatrix 1.19.0.20 were done with link-time optimization. (uploaded last weekend). I'd be interested if anybody wants to compare the speed of the 1000 genome code vs 1.19.0.19 on windows. LTO on linux is 10+% faster. There is a new bug fix in GLM related stuff in snpStats x.x.x.8 . I'd be intereste...

...s missing from all of R 3.1.0, 3.1.1, and 3.1.2. The next thing I am doing is building the replacement for the cairo.dll's in the offical R windows binaries. Just watch out in the next few days in the same directory. ---------- not R-devel related below this point ------ I have finished with snpMatrix 1.19.0.20 5 days ago. Some of you may notice the documentations are already out - 19 months about 400 commit since 1.19.0.19, it comes with a snpStats compatibility mode; when that mode is on, about 1/3 of its internals are swapped to their snpStats-equivalent versions. Initially synchronized to sn...

Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+) e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names': ?new? Error in `row.names<-.data.frame`(`*tmp*`, value = c("1", "new", "new" : duplicate 'row.names' are not...

I have had some fun in the last few days trying to put together an annotated map of China with R and some public GIS data: http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.17.7.11/China_Choropleth_Maps.pdf/download It is done, and rather nice... there are a few issues: - the default pdf() device cannot do CJK with embedded fonts - and cairo_pdf() is not hooked up to Sweave yet. I have had a quick look, and it does not look too complicated, other than the f...

..., "Algorithms and Thailand", which covers text/stream/sequence and spatial algorithms, and the use of Thai language in a vignette. (Chinese/Tibetan/Arabic/Liangshan Yi was covered in a different vignette previously). More on this and emacs's multilingual extension further down. "snpMatrix Tutorial 2007" was the first ever tutorial written in spring 2007 [1]; it was pre-vignette and therefore had all the hapmap/pedfile output recorded verbatim; newly revived to work as a testsuite for input/output of hapmap/ped files (and flaged and fixed a few bugs introduced in the last few ye...

This is somewhat a summary/continuation of an R bug report: (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14645) Illumina's cluster definition files (*.egt) are one of the proprietary and undocumented file formats used by their GenomeStudio line of products for genomic studies. snpMatrix 1.17.0.7 onwards (http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/) contains codes for reading that file format, as well as two example files of such type generated from public data, and also a vignette demonstrating their usefulness and relevance to genomic studies. R svn c...

...or: unprotected object (0x2768b18) encountered (was REALSXP) Error: package/namespace load failed for 'Matrix' Execution halted --------------- I traced to this because "R CMD check --use-gct snpStats" (both 1.1.13 and 1.1.12) segfaults with the same message, and before that, the snpMatrix 1.15.8.4 which includes some of David's newly written ld() ( which depends on Matrix.) If the Matrix package segfaults, David's new ld() isn't useable.

I finally got round to look at a little problem I have - most of the time when I use R I would be using snpMatrix (now part of bioconductor, I wrote a substantial part of), so I had $HOME/.Rprofile to save some typing. Upgrading, switching versions used to work fine with R 2.8 then it broke with 2.9.. Apparently it is because most of SHLIB, INSTALL, etc used to be fairly extensive shell scripts in R 2.8 where...

...DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] "splines" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: snpMatrix survival "1.0.4" "2.30" >

...issue due to a bad interaction for the combination of both the shlib compile-time option and the EL4 runtime environment. (e.g. R 2.4.1 is shipped and bundled with zlib 1.2.3 but EL4 is only equiped with zlib 1.2.1.2...). For the moment I'll just recommend anybody who needs to run my package (snpMatrix in http://www-gene.cimr.cam.ac.uk/clayton/software/) on Redhat EL4 to just build and install R from source, since shlib=no is the default for compiling from source. Anybody has any idea how this strange brokenness of zlib might happen? Hin-Tak Leung

Hi, (somebody would probably yell at me for not checking 2.6.0rc, for which I can only apologize...) Our R package (snpMatrix in http://www-gene.cimr.cam.ac.uk/clayton/software/) is broken rather badly in 2.6.0 ; I have fixed most of it now so a new release is imminent; but I'd like to mention a few things, mostly to summarize my experience and hopefully the 'writing R extensions' document can be updated to r...

Dear, I would like to deal with microarray data, it can run when i deal with little data. However, the amount number of SNP data are 45181, amount numbers of animal are 3081,it can not be allocated 1000Mb memory when i importing them to R Procedure sentence show: m<-matrix(scan("D:/SNPdata.txt"),ncol=nmarkers,byrow=TRUE) Error show: Error: cannot allocate vector of size 1000.0 Mb

snpMatrix package is quite nice (read.plink())

...k and 2.14.1? --- On Sat, 22/10/11, Hin-Tak Leung <htl10 at users.sourceforge.net> wrote: > I have had some fun in the last few > days trying to put together an annotated map of China with R > and some public GIS data: > > http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.17.7.11/China_Choropleth_Maps.pdf/download > > It is done, and rather nice... there are a few issues: > > - the default pdf() device cannot do CJK with embedded > fonts - and cairo_pdf() is not hooked up to Sweave yet. I > have had a quick look, and it does not look too...

...R to cross-compile R packages. (native R for executing R code, win32 R for its R.dll for the cross-compiler's linker to resolve symbols) Go back to R 2.8.x and study the cross-compile instructions and make sure that works, before attempting cross-compile with R 2.9.x . FWIW, I just built win32 snpMatrix against R 2.9.2 last week and released that, and also managed to build the chm windows-help file for the first time.. These days, R packages for different platform only differ by the dll/so (and to a lesser extent, things like the chm file) so you just need to build the dll/so to go from one platfo...

R fails to build with visibility on and gcc 4.9's link time optimzation, because of its practice of building part of it as archive first. Specifically it builds some bundled libraries as archive first, the symbols of which are then entirely invisible in gcc 4.9. The Matrix package also does this awful practice, with CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a . One way of fixing R is:

Hi All, I've been having a little trouble with creating a loop that will run a a series of t.tests for inspection, Below is the code i've tried, and some checks i've looked at. I've used the get(paste()) idea as i was told previously that the use of the eval should try and be avoided. I've run a single syntax to check that my systax is correct and works without any problems