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thierrygosselin / radiator

RADseq Data Exploration, Manipulation and Visualization using R
https://thierrygosselin.github.io/radiator/
GNU General Public License v3.0
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genomic_converter:bed -> genind. strata #182

Closed MeriLaht closed 6 months ago

MeriLaht commented 7 months ago

I'm trying to convert BED file to genind. I am able to do this, but the IDs are stored to both individuals and stratas.

I tested the strata DF which works correclty:

> radiator::summary_strata(strata_df)
Number of strata: 4
Number of individuals: 13

Number of ind/strata:
Sweden = 4
Denmark = 1
Germany = 1
Czech_Republic = 7

Number of duplicate id: 0

But when I run 

ater_LD05 <- radiator::genomic_converter(
  data = "results/bed/snps_ater_merged_m0.2_L0.5.bed",
  strata = strata_df,
  c("genind", "genepop"))

The IDs are counted as stratass Data format of input: plink.bed.file Biallelic data Number of markers: 2407 Number of chromosome/contig/scaffold: 1 Number of strata: 13 Number of individuals: 13

print(ater_LD05$genind$strata)
 INDIVIDUALS STRATA
MA0202      MA0202 MA0202
MA0276      MA0276 MA0276
SCi10        SCi10  SCi10

Session info 

> devtools::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.2 (2022-10-31)
 os       macOS Ventura 13.4
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Stockholm
 date     2024-02-09
 rstudio  2023.06.2+561 Mountain Hydrangea (desktop)
 pandoc   3.1.11 @ /opt/homebrew/bin/pandoc

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────
 package          * version    date (UTC) lib source
 abind              1.4-5      2016-07-21 [1] CRAN (R 4.2.0)
 ade4             * 1.7-22     2023-02-06 [1] CRAN (R 4.2.0)
 adegenet         * 2.1.10     2023-01-26 [1] CRAN (R 4.2.0)
 ape                5.7-1      2023-03-13 [1] CRAN (R 4.2.0)
 backports          1.4.1      2021-12-13 [1] CRAN (R 4.2.0)
 BiocGenerics       0.44.0     2022-11-07 [1] Bioconductor
 Biostrings         2.66.0     2022-11-07 [1] Bioconductor
 bit                4.0.5      2022-11-15 [1] CRAN (R 4.2.0)
 bit64              4.0.5      2020-08-30 [1] CRAN (R 4.2.0)
 bitops             1.0-7      2021-04-24 [1] CRAN (R 4.2.0)
 broom              1.0.5      2023-06-09 [1] CRAN (R 4.2.0)
 cachem             1.0.8      2023-05-01 [1] CRAN (R 4.2.0)
 callr              3.7.3      2022-11-02 [1] CRAN (R 4.2.0)
 car                3.1-2      2023-03-30 [1] CRAN (R 4.2.0)
 carData            3.0-5      2022-01-06 [1] CRAN (R 4.2.0)
 caret            * 6.0-94     2023-03-21 [1] CRAN (R 4.2.0)
 class              7.3-22     2023-05-03 [1] CRAN (R 4.2.0)
 cli                3.6.2      2023-12-11 [1] CRAN (R 4.2.3)
 cluster            2.1.4      2022-08-22 [1] CRAN (R 4.2.2)
 codetools          0.2-19     2023-02-01 [1] CRAN (R 4.2.0)
 colorspace         2.1-0      2023-01-23 [1] CRAN (R 4.2.0)
 combinat           0.0-8      2012-10-29 [1] CRAN (R 4.2.0)
 crayon             1.5.2      2022-09-29 [1] CRAN (R 4.2.0)
 curl               5.0.1      2023-06-07 [1] CRAN (R 4.2.0)
 data.table         1.15.0     2024-01-30 [1] CRAN (R 4.2.3)
 desc               1.4.3      2023-12-10 [1] CRAN (R 4.2.3)
 devtools           2.4.5      2022-10-11 [1] CRAN (R 4.2.0)
 digest             0.6.34     2024-01-11 [1] CRAN (R 4.2.3)
 dplyr            * 1.1.4      2023-11-17 [1] CRAN (R 4.2.3)
 ellipsis           0.3.2      2021-04-29 [1] CRAN (R 4.2.0)
 fansi              1.0.6      2023-12-08 [1] CRAN (R 4.2.3)
 fastmap            1.1.1      2023-02-24 [1] CRAN (R 4.2.0)
 forcats          * 1.0.0      2023-01-29 [1] CRAN (R 4.2.0)
 foreach          * 1.5.2      2022-02-02 [1] CRAN (R 4.2.0)
 fs                 1.6.3      2023-07-20 [1] CRAN (R 4.2.0)
 fst                0.9.8      2022-02-08 [1] CRAN (R 4.2.0)
 fstcore          * 0.9.18     2023-12-02 [1] CRAN (R 4.2.3)
 future             1.33.1     2023-12-22 [1] CRAN (R 4.2.3)
 future.apply       1.11.1     2023-12-21 [1] CRAN (R 4.2.3)
 gam              * 1.22-3     2023-11-29 [1] CRAN (R 4.2.3)
 gdsfmt             1.34.1     2023-04-02 [1] Bioconductor
 generics           0.1.3      2022-07-05 [1] CRAN (R 4.2.0)
 GenomeInfoDb       1.34.9     2023-02-05 [1] Bioconductor
 GenomeInfoDbData   1.2.9      2023-01-30 [1] Bioconductor
 GenomicRanges      1.50.2     2022-12-18 [1] Bioconductor
 ggplot2          * 3.4.4      2023-10-12 [1] CRAN (R 4.2.0)
 ggpubr           * 0.6.0      2023-02-10 [1] CRAN (R 4.2.0)
 ggsignif           0.6.4      2022-10-13 [1] CRAN (R 4.2.0)
 globals            0.16.2     2022-11-21 [1] CRAN (R 4.2.0)
 glue               1.7.0      2024-01-09 [1] CRAN (R 4.2.3)
 gower              1.0.1      2022-12-22 [1] CRAN (R 4.2.0)
 gridExtra        * 2.3        2017-09-09 [1] CRAN (R 4.2.0)
 gtable             0.3.4      2023-08-21 [1] CRAN (R 4.2.0)
 hardhat            1.3.1      2024-02-02 [1] CRAN (R 4.2.3)
 hms                1.1.3      2023-03-21 [1] CRAN (R 4.2.0)
 htmltools          0.5.5      2023-03-23 [1] CRAN (R 4.2.0)
 htmlwidgets        1.6.2      2023-03-17 [1] CRAN (R 4.2.0)
 httpuv             1.6.11     2023-05-11 [1] CRAN (R 4.2.0)
 igraph             1.5.0.1    2023-07-23 [1] CRAN (R 4.2.0)
 ipred              0.9-14     2023-03-09 [1] CRAN (R 4.2.0)
 IRanges            2.32.0     2022-11-07 [1] Bioconductor
 iterators          1.0.14     2022-02-05 [1] CRAN (R 4.2.0)
 label.switching  * 1.8        2019-07-01 [1] CRAN (R 4.2.0)
 later              1.3.1      2023-05-02 [1] CRAN (R 4.2.0)
 lattice          * 0.21-8     2023-04-05 [1] CRAN (R 4.2.0)
 lava               1.7.3      2023-11-04 [1] CRAN (R 4.2.3)
 lifecycle          1.0.4      2023-11-07 [1] CRAN (R 4.2.3)
 listenv            0.9.1      2024-01-29 [1] CRAN (R 4.2.3)
 lpSolve            5.6.18     2023-02-01 [1] CRAN (R 4.2.0)
 lubridate        * 1.9.2      2023-02-10 [1] CRAN (R 4.2.0)
 magrittr           2.0.3      2022-03-30 [1] CRAN (R 4.2.0)
 MASS               7.3-60     2023-05-04 [1] CRAN (R 4.2.0)
 Matrix             1.5-1      2022-09-13 [1] CRAN (R 4.2.2)
 memoise            2.0.1      2021-11-26 [1] CRAN (R 4.2.0)
 mgcv               1.9-0      2023-07-11 [1] CRAN (R 4.2.0)
 mime               0.12       2021-09-28 [1] CRAN (R 4.2.0)
 miniUI             0.1.1.1    2018-05-18 [1] CRAN (R 4.2.0)
 ModelMetrics       1.2.2.2    2020-03-17 [1] CRAN (R 4.2.0)
 munsell            0.5.0      2018-06-12 [1] CRAN (R 4.2.0)
 nlme               3.1-162    2023-01-31 [1] CRAN (R 4.2.0)
 nnet               7.3-19     2023-05-03 [1] CRAN (R 4.2.0)
 parallelly         1.36.0     2023-05-26 [1] CRAN (R 4.2.0)
 patchwork        * 1.1.2      2022-08-19 [1] CRAN (R 4.2.0)
 permute            0.9-7      2022-01-27 [1] CRAN (R 4.2.0)
 pillar             1.9.0      2023-03-22 [1] CRAN (R 4.2.0)
 pkgbuild           1.4.3      2023-12-10 [1] CRAN (R 4.2.3)
 pkgconfig          2.0.3      2019-09-22 [1] CRAN (R 4.2.0)
 pkgload            1.3.4      2024-01-16 [1] CRAN (R 4.2.3)
 plyr               1.8.9      2023-10-02 [1] CRAN (R 4.2.0)
 pROC               1.18.5     2023-11-01 [1] CRAN (R 4.2.0)
 processx           3.8.3      2023-12-10 [1] CRAN (R 4.2.3)
 prodlim            2023.08.28 2023-08-28 [1] CRAN (R 4.2.0)
 profvis            0.3.8      2023-05-02 [1] CRAN (R 4.2.0)
 promises           1.2.0.1    2021-02-11 [1] CRAN (R 4.2.0)
 ps                 1.7.6      2024-01-18 [1] CRAN (R 4.2.3)
 purrr            * 1.0.2      2023-08-10 [1] CRAN (R 4.2.0)
 R6                 2.5.1      2021-08-19 [1] CRAN (R 4.2.0)
 radiator           1.2.9      2024-02-09 [1] Github (thierrygosselin/radiator@c92cc45)
 Rcpp               1.0.12     2024-01-09 [1] CRAN (R 4.2.3)
 RcppCNPy         * 0.2.12     2023-11-27 [1] CRAN (R 4.2.3)
 RCurl              1.98-1.14  2024-01-09 [1] CRAN (R 4.2.3)
 readr            * 2.1.5      2024-01-10 [1] CRAN (R 4.2.3)
 recipes            1.0.9      2023-12-13 [1] CRAN (R 4.2.3)
 remotes          * 2.4.2.1    2023-07-18 [1] CRAN (R 4.2.0)
 reshape2           1.4.4      2020-04-09 [1] CRAN (R 4.2.0)
 rlang              1.1.3      2024-01-10 [1] CRAN (R 4.2.3)
 rpart              4.1.19     2022-10-21 [1] CRAN (R 4.2.2)
 rstatix          * 0.7.2      2023-02-01 [1] CRAN (R 4.2.0)
 rstudioapi         0.15.0     2023-07-07 [1] CRAN (R 4.2.0)
 S4Vectors          0.36.2     2023-03-01 [1] Bioconductor
 scales             1.3.0      2023-11-28 [1] CRAN (R 4.2.3)
 SeqArray           1.38.0     2022-11-07 [1] Bioconductor
 seqinr             4.2-30     2023-04-05 [1] CRAN (R 4.2.0)
 sessioninfo        1.2.2      2021-12-06 [1] CRAN (R 4.2.0)
 shiny              1.7.4.1    2023-07-06 [1] CRAN (R 4.2.0)
 stringi            1.8.3      2023-12-11 [1] CRAN (R 4.2.3)
 stringr          * 1.5.1      2023-11-14 [1] CRAN (R 4.2.3)
 survival           3.5-5      2023-03-12 [1] CRAN (R 4.2.0)
 svglite          * 2.1.1      2023-01-10 [1] CRAN (R 4.2.0)
 systemfonts        1.0.4      2022-02-11 [1] CRAN (R 4.2.0)
 tibble           * 3.2.1      2023-03-20 [1] CRAN (R 4.2.0)
 tidyr            * 1.3.1      2024-01-24 [1] CRAN (R 4.2.3)
 tidyselect         1.2.0      2022-10-10 [1] CRAN (R 4.2.0)
 tidyverse        * 2.0.0      2023-02-22 [1] CRAN (R 4.2.0)
 timechange         0.2.0      2023-01-11 [1] CRAN (R 4.2.0)
 timeDate           4032.109   2023-12-14 [1] CRAN (R 4.2.3)
 tzdb               0.4.0      2023-05-12 [1] CRAN (R 4.2.0)
 urlchecker         1.0.1      2021-11-30 [1] CRAN (R 4.2.0)
 usethis            2.2.2      2023-07-06 [1] CRAN (R 4.2.0)
 utf8               1.2.4      2023-10-22 [1] CRAN (R 4.2.0)
 vctrs              0.6.5      2023-12-01 [1] CRAN (R 4.2.3)
 vegan              2.6-4      2022-10-11 [1] CRAN (R 4.2.0)
 viridis            0.6.4      2023-07-22 [1] CRAN (R 4.2.0)
 viridisLite        0.4.2      2023-05-02 [1] CRAN (R 4.2.0)
 vroom              1.6.5      2023-12-05 [1] CRAN (R 4.2.3)
 withr              3.0.0      2024-01-16 [1] CRAN (R 4.2.3)
 xadmix           * 1.0.0      2022-07-08 [1] CRAN (R 4.2.0)
 xtable             1.8-4      2019-04-21 [1] CRAN (R 4.2.0)
 XVector            0.38.0     2022-11-07 [1] Bioconductor
 zlibbioc           1.44.0     2022-11-07 [1] Bioconductor

 [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
thierrygosselin commented 6 months ago

Hi Meri, could you send over email the necessary files so that I'm able to reproduce your error ?

thierrygosselin commented 6 months ago

reopen the issue if necessary