Displaying 3 results from an estimated 3 matches for "genind".
Did you mean:
genid
2010 May 21
1
S4 method defined but not used
...4 method defined in my package adegenet 1.2-4, with R 2.11.0. As far as I know, the problem is new, and the code implementing the method has not changed for more than a year and worked well so far.
The problem is the following. I define, in the package, a method "[" for the S4 class 'genind'. The method's definition is:
setMethod("[", signature(x="genind", i="ANY", j="ANY", drop="ANY"), function(x, i, j, ..., loc=NULL, treatOther=TRUE, drop=FALSE) {
... ## code of the function
})
When sourcing the code directly from R, this m...
2011 Jul 28
3
R
...orto in Portugal. At this moment I’m
starting to use R, so I have some doubts.
The aim of my analysis is: calculate a pairwise FST matrix from fasta file
and creat a principal component analyses with adegenet package (I use seqinr
and ape package to read this file, then I convert this file into a genind
object with DNA2genind function provide in adegenet package). After convert
my file the pairwise.fst function is not found.
If you could help me would be great.
Greetings: Rui Oliveira
--
-------------------------------------------------------------------
Rui Manuel Oliveira
[[alternative HTM...
2018 Mar 15
3
stats 'dist' euclidean distance calculation
...-c(1, 2, 3, 4, 5+SAMPS:ncol(Mydata))]
locus
# Locus1 Locus2 Locus3
# Samp1 GG <NA> GG
# Samp2 AG CA GA
# Samp3 AG CA GG
# converts geno matrix to genind object (adegenet)
Mydata1 <- df2genind(locus, ploidy = 2, ind.names = ind[1:SAMPS], pop = population[1:SAMPS], sep="")
Mydata1$tab # get stats on newly created genind object
# Locus1.G Locus1.A Locus2.C Locus2.A Locus3.G Locus3.A
# Samp1...