search for: snpstats

Hi, Does anybody know how to obtain the imputed SNP genotype probabilities from the snpStats package? I am interested in using an imputation method implemented in R to be further used in a simulation study context. I have found the snpStats package that seems to contain suitable functions to do so. As far as I could find out from the package vignette examples and its help, it gives th...

...angshanYi/Arabic vignette, which was in reality just Chinese + Cairo graphics. Managed to cross-compile an R package for Mac OS X from Linux; and it seems to be working. See screenshots below. I'd be interested to know if there are less obvious bugs; however numerical difference with native snpStats 1.5.5 is more likely because 1.5.5 is buggy than 1.5.5.1 mis-compiled. Also noticed that R on Mac OS X is universal, with symlinks to the per-arch multiarch dylibs. Is there any plans for R packages to switch over to universal instead of multi-arch? (the sentence below as strictly speaking wron...

...evices-libs-winCairo_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...

...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 snpStats x.x.x.8 - and I already mentioned that it is because of another GLM related bug, found on top of x.x.x.7. Sigh. snpMatrix 1.19.0.20 and snpStat...

...rror : .onLoad failed in loadNamespace() for 'Matrix', details: call: fun(...) error: 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.

...t; http://sourceforge.net/projects/outmodedbonsai/files/Manuals%2C%20Overviews%20and%20Slides%20for%20talks/2013SummerCourse/practicals/with-answers/practical8_survival-clogit-diff.pdf/download >> >> That's the one problem from David's 10 practicals which are not due to bugs in snpStats. Some might find it reassuring that only 3 of the 4 problems with the practicals are due to snpStats bugs. >> >> http://sourceforge.net/projects/outmodedbonsai/files/Manuals%2C%20Overviews%20and%20Slides%20for%20talks/2013SummerCourse/practicals/with-answers/practical7_snpStatsBug-diff...

Dear experts, I am trying to perform an association using snpStats. I have a snp matrix called 'plink' which contains my genotype data (as a list of $genotypes, $map, $fam), and a phenotype data frame which contains the outcomes (outcome1, outcome2,...) I would like to associate with the genotype. My question is, how do I loop through the outcomes? This ty...

Hello, I want to know if there are some functions or packages to solve differential and integral equation using R. Thanks. Shao chunxuan. [[alternative HTML version deleted]]