Question: GWASTools
0
gravatar for Stephanie M. Gogarten
6.7 years ago by
University of Washington
Stephanie M. Gogarten740 wrote:
Dear Uli, Thanks for the suggestion. In GWASTools 1.5.9 (which will become the next release very soon), the "snp.annot" argument in convertNcdfGds should be a SnpAnnotationDataFrame, and the chromosome codes from snp.annot will be preserved in the resulting GDS file. best wishes, Stephanie On 1/16/13 2:42 AM, Ulrich Knief wrote: > Dear Stephanie, > I entered this code and it seems it changes the internal chromosome > coding in SNPRelate after using 'convertNcdfGds'. > > path = "" > geno.nc.file <- "tmp.geno.nc" > ncfile <- paste(path,geno.nc.file,sep="") > gdsfile <- "tmp_geno.gds" > annot1 <- data.frame(pData(scanAnnot1)) > convertNcdfGds(ncfile, gdsfile, sample.annot=annot1) > > ZFwild <- openfn.gds("tmp_geno.gds", readonly=FALSE) > > # change internal chromosome coding > option <- snpgdsOption(autosome.start=1, autosome.end=32) > chrcode <- option$chromosome.code > chr <- snpAnnot$chromosome > for (i in names(chrcode)) chr[snpAnnot$chromosome == i] <- chrcode[[i]] > chr <- as.integer(chr) > chr[is.na(chr)] <- 0 > put.attr.gdsn(index.gdsn(ZFwild, c("snp.chromosome")), > "autosome.start", option$autosome.start) > put.attr.gdsn(index.gdsn(ZFwild, c("snp.chromosome")), > "autosome.end", option$autosome.end) > for (i in 1:length(option$chromosome.code)) { > put.attr.gdsn(index.gdsn(ZFwild, c("snp.chromosome")), > names(option$chromosome.code)[i], > option$chromosome.code[[i]]) > } > sync.gds(ZFwild) > > > Best wishes > Uli > > > > -------- Original Message -------- > Subject: Re: GWASTools > Date: Wed, 16 Jan 2013 10:12:16 +0100 > From: Ulrich Knief <uknief at="" orn.mpg.de=""> > To: Stephanie M. Gogarten <sdmorris at="" u.washington.edu=""> > > > > Dear Stephanie, > sorry to bother you again. I have a problem with defining new chromosome > codes during conversion from GWASTools to SNPRelate. I use the function > 'convertNcdfGds' from the GWASTools package. You cannot specify > differing chromosome names in this function. > Then I tried to change the internal chromosome representations in > SNPRelate with 'snpgdsOption'. But the list output of this function is > only useable for SNPRelate functions while importing data from PLINK or > VCF files (snpgdsBED2GDS, snpgdsVCF2GDS) and not for the > 'convertNcdfGds' function. Am I missing something? > > I am not sure, but I think in your tutorial on data cleaning you made a > mistake on page 47 when plotting heterozygosity in females on the X > chromosome. Shouldn't it be: > female <- scanAnnot$sex == "F" > boxplot(scanAnnot$het.X[female] ~ scanAnnot$population[female], main="X > Chromosome Heterozygosity in Females") > > > Best wishes > Uli > > > > > > > On 1/7/2013 5:46 PM, Stephanie M. Gogarten wrote: >> "anomDetectLOH" may be what you want. Be warned that it takes a long >> time to run. >> >> Stephanie >> >> On 1/6/13 4:19 PM, Uli wrote: >>> Dear Stephanie, >>> thank you very much for your information and support! I really >>> appreciate your help. I will start writing my scripts in GWASTools and >>> SNPRelate the next days. If I come across any bugs then I could contact >>> you again. Are you planning to implement something like PLINKs 'Runs of >>> Homozygosity' tool in the future? >>> >>> Best wishes >>> Uli >>> >>> >>> >>> Am 03.01.2013 22:49, schrieb Stephanie M. Gogarten: >>>> I think Xiuwen may still be on vacation, but I just noticed that the >>>> latest SNPRelate (0.9.8) has the option to change autosome coding. >>>> Look at "?snpgdsOption". >>>> >>>> Stephanie >>>> >>>> On 12/21/12 10:39 AM, Stephanie M. Gogarten wrote: >>>>> Dear Uli, >>>>> >>>>> Xiuwen Zheng is the author of SNPRelate, and as far as I know it still >>>>> has autosomes hard-coded as 1:22. >>>>> >>>>> Xiuwen, do you have any plans to revise SNPRelate so that it can be >>>>> used >>>>> with a different number of autosomes? I just did this in >>>>> GWASTools, so >>>>> I can give you an example. >>>>> >>>>> Stephanie >>>>> >>>>> On 12/20/12 4:23 PM, Uli wrote: >>>>>> Dear Stephanie, >>>>>> thank you very much for this update - which was very fast - and for >>>>>> letting me know! This gives GWASTools a clear advantage over PLINK in >>>>>> model organisms for all the quality checking. Actually, I think I >>>>>> will >>>>>> put together a pipeline that uses GWASTools for quality control >>>>>> and for >>>>>> the detection of trisomies, then SNPRelate for PCA and then either >>>>>> the >>>>>> emma or the GAPIT package (which includes emma) for the association >>>>>> testing. Since SNPRelate was written by your working group as well, >>>>>> does >>>>>> it also accept the new chromosome names? >>>>>> >>>>>> Regards >>>>>> Uli >>>>>> >>>>>> >>>>>> Am 19.12.2012 21:44, schrieb Stephanie M. Gogarten: >>>>>>> Dear Dr. Knief, >>>>>>> >>>>>>> GWASTools 1.5.5 (available here: >>>>>>>http://bioconductor.org/packages/2.12/bioc/html/GWASTools.html) now >>>>>>> allows you to change the chromosome annotations for autosomes. >>>>>>> There >>>>>>> is an example on the GenotypeData man page ("?GenotypeData") for how >>>>>>> to set up a GenotypeData object for a bird species. >>>>>>> >>>>>>> Stephanie >>>>>>> >>>>>>> On 11/15/12 1:50 AM, Ulrich Knief wrote: >>>>>>>> Hello Dr Gogarten, >>>>>>>> I would like to use your R package GWASTools but I am wondering >>>>>>>> whether >>>>>>>> it is possible to change the internal chromosome names. >>>>>>>> Specifically, >>>>>>>> the organism I am studying has more chromosomes than humans and it >>>>>>>> would >>>>>>>> thus be nice to change the chromosome annotations. Since I am >>>>>>>> working on >>>>>>>> a bird species it would also be nice to change X to Z but this >>>>>>>> is not >>>>>>>> absolutely necessary. >>>>>>>> Is that possible? >>>>>>>> >>>>>>>> Regards, >>>>>>>> Ulrich Knief >>>>>> >>> > > > > -- > J. Ulrich Knief > Max Planck Institute for Ornithology > Department of Behavioural Ecology & Evolutionary Genetics > Eberhard-Gwinner-Stra?e, House 7 > 82319 Seewiesen (Starnberg), Germany > Tel.: +49 (0) 8157 932 - 303 > > > >
organism gwastools snprelate • 1.1k views
ADD COMMENTlink written 6.7 years ago by Stephanie M. Gogarten740
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