Thank you for the great package. I think there must be something obvious that I am missing in the setup (so apologise if that is the case but I can seem to find it) because I have seen some similar errors reported here that were fixed in the most recent version, but I still seem to be encountering the problem.
I'm trying to convert a genlight object to a plink file. It failed with my data file (a genlight object created from Dart data) producing the error - Error: Can't subset columns that don't exist. x Column GT doesn't exist. In troubleshooting the problem I found I couldn't get it to work with the test example provided in the dartR package - bandicoot.gl either. So I have been using that to test with.
Data is bi-allelic
Generating PLINK tped/tfam files
Error: Can't subset columns that don't exist.
x Column GT doesn't exist.
Run rlang::last_error() to see where the error occurred.
Computation time, overall: 19 sec
######################### completed genomic_converter ##########################
output of `devtools::session_info()
devtools::session_info()
Session info ----------------------------------------------------------------------
setting value
version R version 4.1.1 (2021-08-10)
os Windows 10
system i386, mingw32
ui Rgui
language (EN)
collate English_Australia.1252
ctype English_Australia.1252
tz Australia/Sydney
date 2021-09-26
// Basic content
@gen: list of 96 SNPbin
@ploidy: ploidy of each individual (range: 2-2)
// Optional content
@ind.names: 96 individual labels
@loc.names: 1000 locus labels
@loc.all: 1000 alleles
@position: integer storing positions of the SNPs
@pop: population of each individual (group size range: 12-29)
@other: a list containing: loc.metrics latlong ind.metrics loc.metrics.flags verbose history
Thank you for the great package. I think there must be something obvious that I am missing in the setup (so apologise if that is the case but I can seem to find it) because I have seen some similar errors reported here that were fixed in the most recent version, but I still seem to be encountering the problem.
I'm trying to convert a genlight object to a plink file. It failed with my data file (a genlight object created from Dart data) producing the error - Error: Can't subset columns that don't exist. x Column
GT
doesn't exist. In troubleshooting the problem I found I couldn't get it to work with the test example provided in the dartR package - bandicoot.gl either. So I have been using that to test with.The command and error produced are below:
Importing data: genlight Calibrating REF/ALT alleles...
Writing tidy data set: test.rad
Preparing data for output
Data is bi-allelic Generating PLINK tped/tfam files Error: Can't subset columns that don't exist. x Column
GT
doesn't exist. Runrlang::last_error()
to see where the error occurred.Computation time, overall: 19 sec ######################### completed genomic_converter ##########################
output of `devtools::session_info()
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DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.1)
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DEoptimR 1.0-9 2021-05-24 [1] CRAN (R 4.1.1)
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ggplot2 3.3.5 2021-06-25 [1] CRAN (R 4.1.1)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.1)
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gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.1)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.1)
gtools 3.9.2 2021-06-06 [1] CRAN (R 4.1.1)
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hms 1.1.0 2021-05-17 [1] CRAN (R 4.1.1)
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igraph 1.2.6 2020-10-06 [1] CRAN (R 4.1.1)
iterators 1.0.13 2020-10-15 [1] CRAN (R 4.1.1)
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knitr 1.34 2021-09-09 [1] CRAN (R 4.1.1)
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MASS 7.3-54 2021-05-03 [2] CRAN (R 4.1.1)
Matrix 1.3-4 2021-06-01 [2] CRAN (R 4.1.1)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.1.1)
mgcv 1.8-36 2021-06-01 [2] CRAN (R 4.1.1)
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pegas 1.0-1 2021-05-17 [1] CRAN (R 4.1.1)
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plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.1)
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sp 1.4-5 2021-01-10 [1] CRAN (R 4.1.1)
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spdep 1.1-11 2021-09-07 [1] CRAN (R 4.1.1)
StAMPP 1.6.3 2021-08-08 [1] CRAN (R 4.1.1)
stringi 1.7.4 2021-08-25 [1] CRAN (R 4.1.1)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.1)
testthat 3.0.4 2021-07-01 [1] CRAN (R 4.1.1)
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tidyr 1.1.3 2021-03-03 [1] CRAN (R 4.1.1)
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withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.1)
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[1] C:/Users/Lneav/Documents/R/win-library/4.1 [2] C:/Program Files/R/R-4.1.1/library
Datafile: bandicoot.gl - example file found in dartR package
// 96 genotypes, 1,000 binary SNPs, size: 7.1 Mb 1705 (1.78 %) missing data
// Basic content @gen: list of 96 SNPbin @ploidy: ploidy of each individual (range: 2-2)
// Optional content @ind.names: 96 individual labels @loc.names: 1000 locus labels @loc.all: 1000 alleles @position: integer storing positions of the SNPs @pop: population of each individual (group size range: 12-29) @other: a list containing: loc.metrics latlong ind.metrics loc.metrics.flags verbose history
Many thanks for the help. Linda