[adegenet-forum] missing data not recognized for partially incomplete genotypes

[Chloe Chen-Kraus]

Hi--

I am creating a genind object for diploid microsatellite data with
df2genind. I indicate that missing values are coded as "000" with
NA.char="000". When I examine the resulting genind object I can see that
genotypes where both alleles are missing are recognized as NA, but "000" is
still recognized as an allele for genotypes that have only one allele
missing.

For example:

> genotypes.df
      Ind Pop     PV1    PV16    PV14    PV15     PV6     PV8
1    A01    A 000/000 275/279 300/306 252/262 264/270 214/218
2    A02    A 155/159 275/291 300/000 252/262 268/268 216/216
3    A03    A 163/163 275/291 000/000 248/256 268/272 216/218
4    A04    A 159/159 275/000 300/312 252/262 270/274 212/220
5    A05    A 000/000 275/283 306/312 252/252 270/272 214/216

> genotypes <- df2genind(genotypes.df[,-(1:2)], ploidy=2, sep="/", ncode=3,
NA.char = "000")

When I check to see if this worked by converting back to a dataframe, I see
that 000/000 genotypes are now recognized as NAs but 000 is still
recognized as an allele for genotypes with only one missing allele.

> genind2df(genotypes, sep="/")
        PV1    PV16    PV14    PV15     PV6     PV8
001    <NA> 275/279 300/306 252/262 264/270 214/218
002 155/159 275/291 300/000 252/262 268/268 216/216
003 163/163 275/291    <NA> 248/256 268/272 218/216
004 159/159 275/000 300/312 252/262 270/274 212/220
005    <NA> 275/283 306/312 252/252 270/272 214/216

> genotypes at all.names
$PV1
[1] "155" "159" "163" "157" "161" "169" "000" "165"

$PV16
 [1] "275" "279" "291" "000" "283" "287" "289" "281" "277" "285" "293"

$PV14
[1] "300" "306" "000" "312" "308" "316" "304" "302" "318"

$PV15
 [1] "252" "262" "248" "256" "250" "258" "246" "266" "254" "264"

$PV6
[1] "264" "270" "268" "272" "274" "266" "280" "276" "000"

$PV8
[1] "214" "218" "216" "212" "220" "222" "224" "000"


Any insights on how to fix this issue would be greatly appreciated. Thanks!

-*Chloe Chen-Kraus*
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