search for: locus1

...lp community, I have another question about filtering datasets. Please consider the following "toy" data matrix example, called "x" for simplicity. There are 20 different individuals ("ID"), with information about the alleles (A,T, G, C) at six different loci ("Locus1" - "Locus6") for each of these 20 individuals. At any single locus (e.g., "Locus1" or "Locus2", ... or "Locus6"), the individuals have either one allele (from the set of A,T,C,G) or one other allele (from the set of A,T,C, G). For example, at Locus1 ind...

...ng data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidean distance is calculated: 3x3 subset used Locus1 Locus2 Locus3 Samp1 GG <NA> GG Samp2 AG CA GA Samp3 AG CA GG The euclidean distance function is defined as: sqrt(sum((x_i - y_i)^2)) My assumption was that the differen...

Hi all, I'm having a problem once again, trying to do something very simple. Consider the following data frame: x <- read.table(textConnection("locus1 locus2 locus3 A T C A T NA T C C A T G"), header = TRUE) closeAllConnections() I am trying to make a new data frame, replacing "A" with "A/A", "T" with "T/T", "G" with "G/G", and "C" with "C/C." Note also the pre...

> 3x3 subset used > Locus1 Locus2 Locus3 > Samp1 GG <NA> GG > Samp2 AG CA GA > Samp3 AG CA GG > > The euclidean distance function is defined as: sqrt(sum((x_i - y_i)^2)) My > as...