[adegenet-forum] importing data frame as a genind object

[Mark Coulson]

My data are structured as follows
C1              C2                     C3              C4
 etc.

Population   Individual           Locus1        Locus2         etc.
PopA           C0001               0205           1326             etc.
PopA           C0002
etc
etc
etc
PopB           X0001
PopB           X0002
etc.
.
.
.
Missing data coded as NA

Issued the following commands

scotdata <- read.table("Scotland_adegenet_no_river_names.txt", header=TRUE,
sep="\t", quote="\"", colClasses="character", stringsAsFactors=FALSE)

scotind <- df2genind(scotdata[,-(1:2)], sep="",
ind.names=scotdata$Individual, pop=scotdata$Population, missing="NA",
ploidy=2, type="codom", ncode=4)


This converted it to a genind format and issuing 'scotind' gave the correct
number of loci, individuals, etc.

However, x <- summary(scotind) gave exactly 10 alleles per locus and
massive differences between Hexp and Hobs. I have since made a modified
genepop file which reads in correctly and gives the correct number of
alleles, Hexp, Hobs, etc. (however see my other post for DAPC issues!). So
I can go with this for now, but routinely would find the dataframe format
above easier to work with given large datasets.

Cheers,
Mark
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