search for: gwaa

I have a few questions about GenABEL, gwaa data. 1) is there a universal way that most GenABEL people use to add more individuals into a 'gwaa' data? For example, I have a 'gwaa' data, but I need to add some dummy parents, for 'gwaa at phdata', it's easy to add these rows, but for 'gwaa at gtdata', I thi...

...ize 900Mb, using windows 32-bit) onto R in the "convert.snp.ped" statement. I am thinking this problem is likely due to the large size of the files & my version of R is not able to handle them, since I can read in smaller files. Second, and the more precedent issue, is with the load.gwaa.data statement. It keeps giving me the error: "more columns than column names". I have tried to read in the .dat file (and alternately the .csv file) without the header, that does not work. I have checked my data-set and there aren't any discernible columns that are missing. Here'...

How to make the gwaa.data file I have the genotype data in plink format As binary and as text file Can anyone assist me ? [[alternative HTML version deleted]]

...es have been replaced with "NA", and all data seems to have matching corresponding header value - each column has a matching column name. What could be the possible underlying problem? I have tried to problem-solve but clearly I am at a loss. Thanks for your help! Code: mix <- load.gwaa.data (phe = "Z:/CCFPhenotypesTAB.dat", gen = "pedmap-0.raw", force = T) -- View this message in context: http://n4.nabble.com/R-error-more-columns-than-column-names-tp1568052p1568052.html Sent from the R help mailing list archive at Nabble.com.

.... It mainly consists of small families (2 or more brothers, father and mother; otherwise only the brothers are given). Genotypes are provided for the largest part of the members, whereas the phenotype is only given for the male individuals. I imported the data using the convert.snp.ped and load.gwaa.data commands. The kinship table was constructed with "makekinship". When I look at the dimensions of the kinship table, it is exactly the same as the number of individuals in my dataset. I also provide you with the following information because maybe that gives a clue on where thing...

...move("simulation.raw") file.remove("permuted.txt") file.remove("permchisq.txt") file.remove("rawoutput.txt") # loading data and bringing in GenABEL format rawfile="simulation.raw" convert.snp.ped(pedfile, mapfile, rawfile) simulation.GenABEL = load.gwaa.data(phenofile = phenofil, genofile = rawfile, force=F,makemap=F,sort=F) pedigree=read.table(pedfile) pedsize=nrow(pedigree) nsnps=(ncol(pedigree)-6)/2 # minor allele count and handling missing genotype data allelic = function(k){ geno=pedigree[,(5+2*k):(6+2*k)] allelic=rowSums(geno==2)-(geno[,1]=...