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

Mark Coulson coulsonmw at gmail.com
Mon Dec 1 14:01:54 CET 2014

My data are structured as follows
C1              C2                     C3              C4

Population   Individual           Locus1        Locus2         etc.
PopA           C0001               0205           1326             etc.
PopA           C0002
PopB           X0001
PopB           X0002
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.

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