search for: heterozygosity

Hi, I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Adagenet converts the DNA sequence into retaining only retaining the polymorphic sites and then calcuates Fst.. but is there any other way to do this? I mean analyse the DNA sequence as it is.. and calculate the statistics? Thanks! [[alternative HTML version...

...ing there. This pseudoreplication constitutes about 12% of all observations. I have information on the number of heterozygous locus per individual, its location, year, population size and number of immigrants at that location, and want to investigate the effect of population size and migration on heterozygosity through time. Heterozygosity, the response variable is a proportion, and I would like to account for the pseudoreplication. Their heterozygosity score will be the same for each sampling, and is constant. I have been trying with a mixed models approach, more specifically glmer (lme4 package) with a...

...tay closer to each other? I've tried to adjust mar option of par but it has a global effect as I see the left margin of the first plot will be adjusted as well. Below is the code fragment: r.par(mfrow=[1,2],mar=[5,4,1,1]) r.plot(x,hets,xlim=[0,105],xlab='Samples(%)',ylab='Heterozygosity(%)',co l=colors,cex=0.6) ... plot(completion,hets,xlim=[40,100],xlab="Sample Completion(%)",ylab="",col=colors,axes=False,cex=0.6) Thanks Zhaoming [[alternative HTML version deleted]]

...ummary(Genotype.914186) Number of samples typed: 52 (72.2%) Allele Frequency: (2 alleles) Count Proportion 1 73 0.7 2 31 0.3 NA 40 NA Genotype Frequency: Count Proportion 1/1 26 0.5 1/2 21 0.4 2/2 5 0.1 NA 20 NA Heterozygosity (Hu) = 0.4225168 Poly. Inf. Content = 0.3309022 tdt(Genotype.914186, MessWith, famid, pid, fatid, motid, sex, affected ) Transmission/disequilibrium test Data: Genotype.914186 Untransmitted allele frequencies, informative transmissions and exact P-values Allele Frequency...

...s framework to fit a standard quantitative genetic model: z(i) = mu(0) + b(S)S(i) + b(H)H(i) + b(SS)S^2(i) + b(HH)H^2(i) + b(SH)S(i)H(i) + block +error where S(i) is the ancestry index (proportional to the expected fraction of parent 2 alleles in individual i based on its cross type), H(i) is the heterozygosity index (proportional to the expected fraction of loci with one allele from parent 1 and one allele from parent 2), b(i) are the regression coefficients and mu(0) is the mean phenotype of the F2 generation of hybrids (reference generation). Non-genetic components of variation are partitioned into ind...

I am aware of the R Genetics Project that developed the R library and software called Bioconductor (http://www.bioconductor.org/ ) . How do the two relate to each other? What is the one that the other is not and vice versa? Can anybody link me to something that answers the question? -- Farrel Buchinsky, MD Pediatric Otolaryngologist Allegheny General Hospital Pittsburgh, PA

...s): Stephan Artmann, Mathias Fuchs License: GPL http://crantastic.org/packages/gsmaRt combined miRNA- and mRNA-testing * HIest (1.0) Maintainer: Unknown Author(s): Ben Fitzpatrick License: GPL (>= 3) http://crantastic.org/packages/HIest Uses likelihood to estimate ancestry and heterozygosity. Evaluates simple hybrid classifications (parentals, F1, F2, backcrosses). Estimates genomic clines. * igraphdata (0.1) Maintainer: Gabor Csardi Author(s): Gabor Csardi <csardi.gabor at gmail.com> License: GPL (>= 2) + file LICENSE http://crantastic.org/packages/igraphdata...

...Best Jordan [[alternative HTML version deleted]] --Forwarded Message Attachment-- From: bluejay948 at gmail.com To: r-help at r-project.org Date: Mon, 23 Aug 2010 12:30:28 +0200 Subject: [R] DNA sequence Fst Hi, I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Adagenet converts the DNA sequence into retaining only retaining the polymorphic sites and then calcuates Fst.. but is there any other way to do this? I mean analyse the DNA sequence as it is.. and calculate the statistics? Thanks! [[alternative HTML...