strata in the AMOVA analysis

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Laia Juliana Muñoz

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Feb 15, 2022, 11:01:23 AM2/15/22
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Hi, I received my SNPs data set from Dart. I am trying to do an AMOVA but my genclone object does not have STRATA. I am following this tutorial https://grunwaldlab.github.io/Population_Genetics_in_R/AMOVA.html for adding a new strata to my object but I have been having this error. Could you help me please

 strata(geneclone) <- data.frame(other(geneclone))
Starting gl.read.dart

Starting utils.read.dart
  Topskip not provided. Setting topskip to 6 .
  Reading in the SNP data
  Detected 2 row format.
Added the following locus metrics:
AlleleID AlleleSequence TrimmedSequence Chrom_Bacterias_NCBI ChromPos_Bacterias_NCBI AlnCnt_Bacterias_NCBI AlnEvalue_Bacterias_NCBI SNP SnpPosition CallRate OneRatioRef OneRatioSnp FreqHomRef FreqHomSnp FreqHets PICRef PICSnp AvgPIC AvgCountRef AvgCountSnp RepAvg .
Number of rows per clone (should be only  2 s): 2
 Recognised: 198 individuals and 86911  SNPs in a 2 row format using YFT2.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  198 matching ids out of 198 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
 Data read in. Please check carefully the output above
  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)
Completed: gl.read.dart
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE,  :
  arguments imply differing number of rows: 86911, 198, 1

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