[adegenet-forum] Error with strata

[Zhian Kamvar]

This question was cross-posted an hour and a half later to
https://github.com/thibautjombart/adegenet/issues/360 where I saw it first
and answered to the best of my ability there.

I receive a daily digest of messages from this forum, so it will likely
take a day or more for me to answer them. Please refrain from cross-posting
in the future.

Best,
Zhian

On Fri, Apr 12, 2024 at 9:05 AM <
adegenet-forum-request at lists.r-forge.r-project.org> wrote:

>
> Date: Fri, 12 Apr 2024 11:04:56 -0500
> From: Laia Juliana Mu?oz <laiajulianamu at gmail.com>
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] Error with strata
> Message-ID:
>         <CAHxmJvKFBJ+Qv_BEOrPf45mG=9XR8=
> KVPZRhPyH0sDX4ZXCtgg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi I am trying to create a strata for running an AMOVA. I am using a
> Genlight object but for some reason I am having the error below.
>  Can somebody help me, please?
>
>
> > strata(gl) <- data.frame(other(gl))Starting gl.read.dart Starting
> utils.read.dart   Topskip not provided. Setting topskip to 6 .  Reading in
> the SNP data  Detected 2 row format.Number of rows per clone (should be
> only  2 s): 2  Added the following locus metrics:AlleleID CloneID
> AlleleSequence TrimmedSequence SNP SnpPosition CallRate OneRatioRef
> OneRatioSnp FreqHomRef FreqHomSnp FreqHets PICRef PICSnp AvgPIC AvgCountRef
> AvgCountSnp RepAvg .Recognised: 479 individuals and 76246  SNPs in a 2 row
> format using Report_DTu24-9051_2_moreOrders_SNP_1.csv Completed:
> utils.read.dart Starting utils.dart2genlight Starting conversion....Format
> is 2 rows.Please note conversion of bigger data sets will take some
> time!Once finished, we recommend to save the object using save(object,
> file="object.rdata")Adding individual metrics: meta2.csv .  Ids for
> individual metadata (at least a subset of) are matching!  Found  479
> matching ids out of 479 ids provided in the ind.metadata file.  Added
> population a
>  ssignments.  Added latlon data. Added  id  to the other$ind.metrics slot.
>   Added  pop  to the other$ind.metrics slot.
>   Added  lat  to the other$ind.metrics slot.
>   Added  lon  to the other$ind.metrics slot.Completed:
> utils.dart2genlight    479 rows and 76246 columns of data read  Read
> depth calculated and added to the locus metrics  Minor Allele
> Frequency (MAF) calculated and added to the locus metrics
> Recalculating locus metrics provided by DArT (optionally
> specified)Starting gl.compliance.check   Processing genlight object
> with SNP data  Checking coding of SNPs    SNP data scored NA, 0, 1 or
> 2 confirmed  Checking for population assignments    Population
> assignments confirmed  Checking locus metrics and flags  Recalculating
> locus metrics  Checking for monomorphic loci    No monomorphic loci
> detected  Checking for loci with all missing data    No loci with all
> missing data detected  Checking whether individual names are unique.
> Checking for individual metrics    Individual metrics confirmed
> Spelling of coordinates checked and changed if necessary to
>  lat/lonCompleted: gl.compliance.check Completed: gl.read.dart Error
> in utils.check.datatype(x, verbose = verbose) :
>   Fatal Error: inappropriate object passed to function, found list
> expecting genlight or SNP or SilicoDArT> strata(gi) <-
> data.frame(other(gi))Starting gl.read.dart Starting utils.read.dart
> Topskip not provided. Setting topskip to 6 .  Reading in the SNP data
> Detected 2 row format.Number of rows per clone (should be only  2 s):
> 2  Added the following locus metrics:AlleleID CloneID AlleleSequence
> TrimmedSequence SNP SnpPosition CallRate OneRatioRef OneRatioSnp
> FreqHomRef FreqHomSnp FreqHets PICRef PICSnp AvgPIC AvgCountRef
> AvgCountSnp RepAvg .Recognised: 479 individuals and 76246  SNPs in a 2
> row format using Report_DTu24-9051_2_moreOrders_SNP_1.csv Completed:
> utils.read.dart Starting utils.dart2genlight Starting
> conversion....Format is 2 rows.Please note conversion of bigger data
> sets will take some time!Once finished, we recommend to save the
> object using save(object, file="object.rdata")Adding individual
> metrics: meta2.csv .  Ids for individual metadata (at least a subset
> of) are matching!  Found  479 matching ids out of 479 ids provided in
> the ind.metadata file.  Added population assignments.  Added latlon
> data. Added  id  to the other$ind.metrics slot.
>   Added  pop  to the other$ind.metrics slot.
>   Added  lat  to the other$ind.metrics slot.
>   Added  lon  to the other$ind.metrics slot.Completed:
> utils.dart2genlight    479 rows and 76246 columns of data read  Read
> depth calculated and added to the locus metrics  Minor Allele
> Frequency (MAF) calculated and added to the locus metrics
> Recalculating locus metrics provided by DArT (optionally
> specified)Starting gl.compliance.check   Processing genlight object
> with SNP data  Checking coding of SNPs    SNP data scored NA, 0, 1 or
> 2 confirmed  Checking for population assignments    Population
> assignments confirmed  Checking locus metrics and flags  Recalculating
> locus metrics  Checking for monomorphic loci    No monomorphic loci
> detected  Checking for loci with all missing data    No loci with all
> missing data detected  Checking whether individual names are unique.
> Checking for individual metrics    Individual metrics confirmed
> Spelling of coordinates checked and changed if necessary to
>  lat/lonCompleted: gl.compliance.check Completed: gl.read.dart Error
> in utils.check.datatype(x, verbose = verbose) :
>   Fatal Error: inappropriate object passed to function, found list
> expecting genlight or SNP or SilicoDArT
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