adegenet
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thibautjombart
Strata problem
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/lon
Completed: 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/lon
Completed: 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
I believe this might be a problem from the {dartR} package maintained by @green-striped-gecko (who might be able to suggest a better forum for this question) because none of the output shown or errors exist in {adegenet}.
It looks like the error is coming from a function in {dartR} called utils.check.datatype.
It would be helpful if you could provide any of the following:
- the code for how you created the
globject - the output of
sessionInfo() - the output of
class(gl) - the output of
class(other(gl))
Hi Zhian, thank you for your response. Below are the answers:
-
genlight object
gl <- gl.read.dart( filename="Report_DTu24-9051_2_moreOrders_SNP_1.csv", ind.metafile="meta2.csv") 2. R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C LC_TIME=English_United States.utf8
time zone: America/Chicago tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] poppr_2.9.6 pegas_1.3 ape_5.7-1 dartR.captive_0.90 dartR.spatial_0.89 dartR.popgen_0.88 dartR.sim_0.89 [8] dartRverse_0.51 dartR.base_0.88 dartR.data_1.0.4 dplyr_1.1.4 ggplot2_3.5.0.9000 adegenet_2.1.10 ade4_1.7-22
loaded via a namespace (and not attached): [1] DBI_1.2.2 gdsfmt_1.38.0 gridExtra_2.3 polysat_1.7-7 remotes_2.5.0 permute_0.9-7 [7] rlang_1.1.3 magrittr_2.0.3 e1071_1.7-14 compiler_4.3.2 mgcv_1.9-0 maps_3.4.2 [13] vctrs_0.6.5 reshape2_1.4.4 stringr_1.5.1 profvis_0.3.8 pkgconfig_2.0.3 crayon_1.5.2 [19] SNPRelate_1.36.1 fastmap_1.1.1 ellipsis_0.3.2 utf8_1.2.4 promises_1.2.1 sessioninfo_1.2.2 [25] purrr_1.0.2 cachem_1.0.8 seqinr_4.2-36 pak_0.7.2 later_1.3.2 terra_1.7-71 [31] parallel_4.3.2 cluster_2.1.6 R6_2.5.1 stringi_1.8.3 boot_1.3-30 pkgload_1.3.4 [37] gdistance_1.6.4 Rcpp_1.0.12 iterators_1.0.14 fields_15.2 usethis_2.2.3 httpuv_1.6.14 [43] Matrix_1.6-1.1 splines_4.3.2 igraph_2.0.2 tidyselect_1.2.1 rstudioapi_0.16.0 vegan_2.6-4 [49] doParallel_1.0.17 codetools_0.2-20 miniUI_0.1.1.1 pkgbuild_1.4.4 lattice_0.21-9 tibble_3.2.1 [55] plyr_1.8.9 shiny_1.8.1.1 withr_3.0.0 sf_1.0-16 units_0.8-5 proxy_0.4-27 [61] urlchecker_1.0.1 xml2_1.3.6 pillar_1.9.0 BiocManager_1.30.22 KernSmooth_2.23-22 foreach_1.5.2 [67] generics_0.1.3 sp_2.1-3 hierfstat_0.5-11 munsell_0.5.1 scales_1.3.0 xtable_1.8-4 [73] class_7.3-22 glue_1.7.0 tools_4.3.2 radiator_1.3.0 data.table_1.15.0 dotCall64_1.1-1 [79] fs_1.6.3 melfuR_1.1 grid_4.3.2 tidyr_1.3.1 devtools_2.4.5 colorspace_2.1-0 [85] nlme_3.1-163 patchwork_1.2.0 raster_3.6-26 StAMPP_1.6.3 LEA_3.14.0 cli_3.6.2 [91] spam_2.10-0 fansi_1.0.6 viridisLite_0.4.2 ggdendro_0.2.0 gtable_0.3.4 digest_0.6.35 [97] classInt_0.4-10 htmlwidgets_1.6.4 memoise_2.0.1 htmltools_0.5.7 lifecycle_1.0.4 dismo_1.3-14 [103] mime_0.12 MASS_7.3-60
class(gl)[1] "genlight" attr(,"package") [1] "adegenet"
class(other(gl))[1] "list"
On Fri, 12 Apr 2024 at 13:04, Zhian N. Kamvar @.***> wrote:
I believe this might be a problem from the {dartR} package maintained by @green-striped-gecko https://github.com/green-striped-gecko (who might be able to suggest a better forum for this question) because none of the output shown or errors exist in {adegenet}.
It looks like the error is coming from a function in {dartR} called utils.check.datatype.
It would be helpful if you could provide any of the following:
- the code for how you created the gl object
- the output of sessionInfo()
- the output of class(gl)
- the output of class(other(gl))
— Reply to this email directly, view it on GitHub https://github.com/thibautjombart/adegenet/issues/360#issuecomment-2052229432, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALV6WJNQW2CJEK42NIILHBTY5AOZZAVCNFSM6AAAAABGEN5W66VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJSGIZDSNBTGI . You are receiving this because you authored the thread.Message ID: @.***>
Thank you for providing the code, @laiajulianamu. Looking into the dartR.base::gl.read.dart() function, I think your problem is that the contents of the @other slot is not a data frame of population strata. That function calculates locus-based statistics and strata() assumes individual based population assignments.
However, digging a little further, it looks like a metadata file is required and any column that couldn't be assigned to individual ID, population, or lat/lon is placed in @other$ind.metrics. Perhaps your solution is this if you had columns of strata in "meta2.csv"
strata(gl) <- other(gl)$ind.metrics
@green-striped-gecko, please let me know if my assumptions are correct.
Hi Zhian,
No, I was not able to run it :(
On Sun, 5 May 2024 at 15:19, Zhian N. Kamvar @.***> wrote:
Checking in to see if the solution has worked for you @laiajulianamu https://github.com/laiajulianamu
— Reply to this email directly, view it on GitHub https://github.com/thibautjombart/adegenet/issues/360#issuecomment-2094935916, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALV6WJOHYEY7V6VLAJEEO6TZA2H53AVCNFSM6AAAAABGEN5W66VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJUHEZTKOJRGY . You are receiving this because you were mentioned.Message ID: @.***>
@green-striped-gecko, since this originates from the dartR suite, would you be able to provide some insight?
@laiajulianamu Do you get the same error or a different error after you run the commands?
I am having the same error. Thank you for asking. Best, Laia
On Mon, 6 May 2024 at 11:24, Zhian N. Kamvar @.***> wrote:
@green-striped-gecko https://github.com/green-striped-gecko, since this originates from the dartR suite, would you be able to provide some insight?
@laiajulianamu https://github.com/laiajulianamu Do you get the same error or a different error after you run the commands?
— Reply to this email directly, view it on GitHub https://github.com/thibautjombart/adegenet/issues/360#issuecomment-2096435306, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALV6WJL6NUGFQHHLIAAU7NTZA6VD7AVCNFSM6AAAAABGEN5W66VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJWGQZTKMZQGY . You are receiving this because you were mentioned.Message ID: @.***>