Hi!
I am trying to analyse my data using amova
(http://www.oga-lab.net/RGM2/func.php?rd_id=pegas:amova):
My input to R is a DNA sequence file, format=fasta
dna<- read.dna("XX.fasta", format="fasta") #left other options as
default
d<- dist.dna(dna, model="raw")
g<- read.table("XXX.design")
Load necessary libraries:
library(pegas)
Loading required package: adegenet
Loading required package: MASS
Loading required package: ade4
Running Amova:
amova(d ~ g, nperm = 100)
Error in FUN(X[[1L]], ...) : 'bin' must be numeric or a factor
How can I solve this "bin" problem?
I think it might be a problem with the g variabel. In the example they
type
g <- factor(c(rep("A", 7), rep("B", 8)))
I cannot find any information about what this c(rep....) does. Do
anyone know about a proper manual for the amova function?
My input file for g looks like this:
sequenceA 1
sequenceB 1
sequenceC 1
.
.
.
.
sequenceD 5
.
.
sequenceE 9
sequenceF 9
Where sequenceA is in group 1, sequenceD is in group 5 and so on...
If I type is.factor(g)
I get FALSE
I have also checked that the d (a matrix file) is a numeric file. It
should be correct.
is.numeric(d)
TRUE
Any help will be very much appreciated!
Cheers,
Hanne
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