search for: snpdata

Displaying 3 results from an estimated 3 matches for "snpdata".

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2011 Apr 14
0
extract p-value from mixed model in kinship package
..., 5), rep(4, 5), rep(6, 5), rep(8, 10), rep(10, 10), rep(12, 10), rep(14, 10), rep(16, 10), rep(18, 10), rep(20, 10), rep(22, 10) ) ped <- data.frame(id, dadid, momid) cfam <- makefamid(ped$id,ped$momid, ped$dadid) kmat <- makekinship(cfam, ped$id, ped$momid, ped$dadid) set.seed(3456) SNPdata <- c(1:1000) dat <- sample(c(-1,0,1), 10000, replace = TRUE) snpmat<- data.frame(matrix(dat, ncol = 100)) names(snpmat) <- c(paste ("VR",1:100, sep='' )) yvar <- rnorm(100, 30, 5) mydata <- data.frame(trait1, covtrait, snpmat) fmod <- lmekin(y~ mydata[,i...
2009 Oct 19
1
How to import the large data into 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 Is there any way to import these data and calculations, i am very anxious. Thank you very much. Best regards. Chen
2006 Apr 06
4
Reshaping genetic data from long to wide
Bottom Line Up Front: How does one reshape genetic data from long to wide? I currently have a lot of data. About 180 individuals (some probands/patients, some parents, rare siblings) and SNP data from 6000 loci on each. The standard formats seem to be something along the lines of Famid, pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2, locus2Allele1, locus2Allele2, etc In other