genomic_covertor() issue converting from gtype to other formats: 'ids' column does not exist

[mariaemilyd]

Hi Thierry,

I've found a possible bug in genomic_convertor() where gtype files can't be converted to other data types becuase genomic_convertor does not find an "ids" column. strataG::df2gtype() calls the id column "id" not "ids", which may be the issue?

library(strataG) # v 2.4.9.10
library(radiator) # v 1.1.7

msat <- read.csv("R.tarandus.kluetsch.2017.msat.gtype.csv")

gtype <- df2gtypes(
  msat,
  ploidy = 2,
  id.col = 1,
  strata.col = 2,
  loc.col = 3
)

genomic_converter(gtype, strata = NULL, output = "structure", filename = "my_str_file.str")

Error message:

Execution date@time: 20201201@0938 Folder created: 01_radiator_genomic_converter_20201106@0938 Function call and arguments stored in: radiator_genomic_converter_args_20201106@0938.tsv Filters parameters file generated: filters_parameters_20201106@0938.tsv

Importing data

Error: Can't rename columns that don't exist. x Column ids doesn't exist. Run rlang::last_error() to see where the error occurred.

Computation time, overall: 0 sec

Computation time, overall: 0 sec ######################### completed genomic_converter #######

 sessionInfo()

R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 14393)

Matrix products: default locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] radiator_1.1.7 strataG_2.4.910

loaded via a namespace (and not attached): [1] tidyr_1.1.1 splines_4.0.2 gtools_3.8.2 assertthat_0.2.1 shiny_1.5.0
[6] expm_0.999-5 sp_1.4-2 yaml_2.2.1 LearnBayes_2.15.1 progress_1.2.2
[11] pillar_1.4.6 lattice_0.20-41 glue_1.4.1 quadprog_1.5-8 phangorn_2.5.5
[16] digest_0.6.25 promises_1.1.1 colorspace_1.4-1 htmltools_0.5.0 httpuv_1.5.4
[21] Matrix_1.2-18 plyr_1.8.6 pkgconfig_2.0.3 raster_3.4-5 gmodels_2.18.1
[26] purrr_0.3.4 xtable_1.8-4 scales_1.1.1 gdata_2.18.0 later_1.1.0.1
[31] tibble_3.0.3 mgcv_1.8-31 generics_0.0.2 ggplot2_3.3.2 ellipsis_0.3.1
[36] apex_1.0.4 cli_2.0.2 magrittr_1.5 crayon_1.3.4 mime_0.9
[41] deldir_0.1-28 evaluate_0.14 fansi_0.4.1 nlme_3.1-148 MASS_7.3-51.6
[46] class_7.3-17 vegan_2.5-6 data.table_1.13.2 tools_4.0.2 prettyunits_1.1.1 [51] hms_0.5.3 lifecycle_0.2.0 stringr_1.4.0 munsell_0.5.0 cluster_2.1.0
[56] ade4_1.7-16 compiler_4.0.2 e1071_1.7-3 rlang_0.4.7 classInt_0.4-3
[61] units_0.6-7 grid_4.0.2 rstudioapi_0.11 igraph_1.2.5 rmarkdown_2.3
[66] boot_1.3-25 gtable_0.3.0 codetools_0.2-16 DBI_1.1.0 reshape2_1.4.4
[71] R6_2.4.1 knitr_1.29 dplyr_1.0.2 fastmap_1.0.1 seqinr_3.6-1
[76] fastmatch_1.1-0 adegenet_2.1.3 spdep_1.1-5 readr_1.3.1 permute_0.9-5
[81] KernSmooth_2.23-17 ape_5.4-1 stringi_1.4.6 parallel_4.0.2 Rcpp_1.0.5
[86] vctrs_0.3.2 sf_0.9-6 spData_0.3.8 tidyselect_1.1.0 xfun_0.16
[91] coda_0.19-3

R script "radiator_error.r" and associated microsatellite data in my test_repo here: https://github.com/mariaemilyd/test_repo

Thanks,

Maria

[thierrygosselin]

Dear Maria, sorry about the bug you're experiencing with radiator. I'll have a look at this today

Best, Thierry

[thierrygosselin]

Eric must have changed the internal naming of his gtypes columns... it's no longer ids and strata, it's now id and stratum.

The problem is now fixed in radiator and will be in the next release today (v. 1.1.9).

[thierrygosselin]

These test with your data works for me:

library(radiator)
library(strataG)
msat <- read.csv("R.tarandus.kluetsch.2017.msat.gtype.csv")
gtype <- df2gtypes(
  msat,
  ploidy = 2,
  id.col = 1,
  strata.col = 2,
  loc.col = 3
)
test1 <- radiator::tidy_gtypes(data = gtype)
test2 <- radiator::genomic_converter(data = gtype, strata = NULL, output = "structure", filename = "my_str_file")

[mariaemilyd]

Hi Thierry,

Thanks, I think it worked? Got this warning message: Warning message: In data.table::melt.data.table(data = ., id.vars = cols, measure.vars = measure_vars, : 'measure.vars' [SPLIT_VEC, A1, A2, ...] are not all of the same type. By order of hierarchy, the molten data value column will be of type 'character'. All measure variables not of type 'character' will be coerced too. Check DETAILS in ?melt.data.table for more on coercion.

I also attach the output file as txt, as I am not sure if it has come out right - looks different to what I was expecting. There are many 1s, 2s, and 3s instead of 3 digit microsat alleles?

Thanks very much!

my_str_file.txt

[thierrygosselin]

Ok so it's not normal. Having a look at it right now, the warning message is normal and will be turned off

[thierrygosselin]

the problem is that the microsatellite format is inconsistent, sometimes you have 3 digits and sometimes it's 2 digits... so many flavours .... I remember working on microsatellite during MSc and PhD... I'm really not nostalgic about those days...😬

[mariaemilyd]

Ah that makes sense, I have noticed that before! Yes I'm using someone else's published data which doesn't help either. If genomic_convertor() can't handle that silly format then don't worry, I can try making my own function!

[thierrygosselin]

It will work, I added a piece of code that will pad with 0 anything shorter than 3 So your microsat alleles: "88" "89" "90" "91" "92" "94" "95" "96" "97" "98" "99" will have 0 in front

[mariaemilyd]

Great, thanks!

[thierrygosselin]

Should be fixed with the latest release.

msat <- read.csv("R.tarandus.kluetsch.2017.msat.gtype.csv")

gtype <- df2gtypes(
  msat,
  ploidy = 2,
  id.col = 1,
  strata.col = 2,
  loc.col = 3
)

data <- radiator::tidy_gtypes(data = gtype)

test1 <- radiator::write_structure(data)
test2 <- radiator::genomic_converter(data = gtype, output = "structure")

[mariaemilyd]

Yup, all looks great! Thanks so much for your help.