[adegenet-forum] Error with strata

[Laia Juliana Muñoz]

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 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> 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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