similar to: generic genotype calling algorithm?

Displaying 20 results from an estimated 3000 matches similar to: "generic genotype calling algorithm?"

2008 Jan 21
2
reordering huge data file
Dear R-experts, My problem is how to handle a 10GB data file containing genotype data. The file is in a particular format (Illumina final report) and needs to be altered and merged with phenotype data for further analysis. PERL seems to be an frequently used solution for this type of work, however I am inclined to think it should be doable with R. How do I open a text-file, line by line,
2006 Dec 31
1
Genotype importing from Sequenom
Sequenom has an odd format of calling a SNP genotype gg [1] "C" "GA" "A" "C" "C" "AG" "C" "C" "T" "G" homozygous A is called A and heterozygous is called AT The genetics package cannot handle the fact that some genotypes are declared with 2 letter while other are declared with only 1.
2011 Oct 08
1
HWEBayes, swapping the homozygotes genotype frequencies
I evaluated the Bayes factor in the k=2 allele case with a "triangular" prior under the null as in the example in the help file: HWETriangBF2(nvec=c(88,10,2)) [1] 0.4580336 When I swap the n11 entry and n22 entry of nvec, I received totally different Bayes factor: > > HWETriangBF2(nvec=c(2,10,88)) [1] 5.710153 > In my understanding, defining the genotype frequency as
2009 Apr 27
3
Cannot clean infinite values
Hello all, I have to import numeric data from file but found it contains Infinite values which need to be eliminated. I tried to replace them in this way: data[which(data=="-Inf")] <- -0.3 data[which(data=="+Inf")] <- 0.3 But, somehow, the Infinite values stayed there. Any suggestions? regards, N. -- View this message in context:
2009 Apr 26
2
THE EQUIVALENT OF SQL INNER TABLE JOIN IN R
Hello all, Apologize for the newbie question. What's the easiest way to do a SQL inner table join in R? Say I have a table containing column names A, B, C and another which has columns named C, D, E. I would like to do an inner table join on C and produce a table A, B, C, D, E. thanks a lot, N. -- View this message in context:
2012 Jun 12
2
Error in sort(abs(diff(genomdat)))[1:n.keep] : only 0's may be mixed with negative subscripts
Hello everyone, I`m trying to normalize and analize an illumina SNP array. But when i`m trying to segmentate i`m getting an error: Error in sort(abs(diff(genomdat)))[1:n.keep] : only 0's may be mixed with negative subscripts. I`ve tried everything to fix this but the error still occours. Can anybody give me a tip? Thanks in advance! -- View this message in context:
2007 Apr 23
1
Dominance in qtl model
Hi, I'm using R for a QTL analysis of SNP data. I was wondering if anyone had any advice on fitting a dominance effect into the following function; > myfun4 function (x) { x <- scan(con, nmax=169) y <- unique(x[which(!is.na(x))]) if(length(y)>1) { summary(lme(Ad ~ x, random= ~1|sire, na.action="na.omit")) } else {print("no.infomation")} } Con is the
2009 Nov 09
1
Using something like the "by" command, but on rows instead of columns
Hello R Forum users, I was hoping someone could help me with the following problem. Consider the following "toy" dataset: Accession SNP_CRY2 SNP_FLC Phenotype 1 NA A 0.783143079 2 BQ A 0.881714811 3 BQ A 0.886619488 4 AQ B 0.416893034 5 AQ B 0.621392903 6 AS B 0.031719125 7 AS NA 0.652375037 "Accession"
2006 Dec 29
1
Genotypes are not all the same
I have been merrily using the genetics package and more specifically have been using the makeGenotypes and genotypes function. I check my accomplishments by going > class(g2) [1] "genotype" "factor" and likewise > class(g1) [1] "genotype" "factor" Yet when I execute a command such as allele count I get this > allele.count(g1) D I [1,]
2006 May 02
4
Repeating tdt function on thousands of variables
I am using dgc.genetics to perform TDT analysis on SNP data from a cohort of trios. I now have a file with about 6008 variables. The first few variables related to the pedigree data such as the pedigree ID the person ID etc. Thereafter each variable is a specific locus or marker. The variables are named by a pattern such as "Genotype.nnnnn" with nnnnn corresponding to a number which
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
2012 Jun 14
1
Can someone recommend a package for SNP cluster analysis of Fluidigm microarrays?
I know that there are quite a few packages out that there for cluster analysis. The problem that I am facing is finding a package that will not incorporate all my samples into clusters but just the samples that fit a threshold (that I have not set yet and may need help finding the right level) for genotyping. It should be able to "no call" samples outside the clusters. It also needs to
2006 Jun 05
3
Fastest way to do HWE.exact test on 100K SNP data?
Hi everyone, I'm using the function 'HWE.exact' of 'genetics' package to compute p-values of the HWE test. My data set consists of ~600 subjects (cases and controls) typed at ~ 10K SNP markers; the test is applied separately to cases and controls. The genotypes are stored in a list of 'genotype' objects, all.geno, and p-values are calculated inside the loop over all
2009 Aug 31
1
permutation test - query
Hi, My query is regarding permutation test and reshuffling of genotype/phenotype data I have been using the haplo.stats package of R. for haplotype analysis and I would like to perform an analysis which I'm requesting your advice. I have a data set of individuals genotyped for 12 SNP and a dichotomous phenotype. At first, I have tested each of those SNP independently in order to bypass
2007 Oct 02
1
Trouble obtaining results from a loop
#Hello, #I have a question about obtaining results from a loop I have written. #Below is a sample of individual genotypes from a genetic question I am working on called "P.genotype.sample ". P.genotype.sample<-matrix(10,10,10) P.genotype.sample[,1]<-c(2,2,1,5,1,1,5,6,1,3) P.genotype.sample[,2]<-c(6,3,3,6,8,1,6,7,2,3) P.genotype.sample[,3]<-c(2,2,2,3,3,2,2,2,3,3)
2010 Feb 12
1
"drop if missing" command?
This will probably seem very simple to experienced R programmers: I am doing a snp association analysis and am at the model-fitting stage. I am using the Stats package's "drop1" with the following code: ##geno is the dataset ## the dependent variable (casectrln) is dichotomous and coded 0,1 ## rs743572_2 is one of the snps (which is coded 0,1,2 for the 3 genotypes)
2007 Sep 26
1
Paste a matrix column in pairwise fashion with other columns?
#Hello, #I have would like to paste a single column of a matrix # in pair wise fashion with other columns based upon # even and odd column numbers. # I can do it in a very clunky fashion and I know there # must be a better way. below is a sample matrix and my extremely # clunky code that gets the job done for a small matrix, but i plan to # do this on a much grander scale. any help would be very
2006 Feb 15
1
no convergence using lme
Hi. I was wondering if anyone might have some suggestions about how I can overcome a problem of "iteration limit reached without convergence" when fitting a mixed effects model. In this study: Outcome is a measure of heart action Age is continuous (in weeks) Gender is Male or Female (0 or 1) Genotype is Wild type or knockout (0 or 1) Animal is the Animal ID as a factor
2007 Aug 24
3
Merging two files together in R
Hi, Thanks in advance for reading this post. I received some affymetrix genotyping data back recently (250K, Nsp array)…However, in order for me to do any analysis on this data set, I need to add append the annotation file to it. Basically I want to do something that looks like this: Snpfile(tab delimited): SNPID Genotype X Y 123 AA 13.4 1.2
2005 Apr 05
2
cat bailing out in a for loop
Dear All, I am trying to calculate the Hardy-Weinberg Equilibrium p-value for 42 SNPs. I am using the function HWE.exact from the package "genetics". In order not to do a lot of coding "by hand", I have a for loop that goes through each column (each column is one SNP) and gives me the p.value for HWE.exact. Unfortunately some SNP have reached fixation and HWE.exact requires a