Closed MboiTui closed 3 years ago
MboiTui
commented
3 years ago 5. Further information If i instead filter for long distance ld, the same error is returned after the completion of filter_ld Error = 'Error: $ operator is invalid for atomic vectors'
thierrygosselin
commented
3 years ago I'm unable to reproduce the error you're getting with my data. Your's in incomplet if I want to run the same code, I'll need the strata file you used.
Re-open the issue if this is still relevant for you
jcaccavo
commented
1 year ago I am having this same issue, both when filtering for long distance ld and when not.
Sex-ratio (F/M): 1.53
Error in SeqArray::seqGetData(data, "annotation/format/DP")$data :
$ operator is invalid for atomic vectors
Computation time, overall: 6581 sec
############################ completed sexy_markers ############################Similarly, I am running the sexy_markers function interactively. The input is a vcf file produced by Stacks. I checked that the strata file was read in properly with summary_strata.
You can download the original .csv file I used to create the strata file here.
I prepared this .csv file for use as the strata file, and checked its validity, as follows:
strata_sex <- "dmawsoni_sex.csv"
strata_sex <- readr::read_csv(strata_sex)
# Rows: 109 Columns: 2
# ── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
# Delimiter: ","
# chr (2): INDIVIDUALS, STRATA
#
# ℹ Use `spec()` to retrieve the full column specification for this data.
# ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.pop.levels_sex <- c("M","F","U")
strata_sex$STRATA <- factor(strata_sex$STRATA, levels = pop.levels_sex)
strata_sex <- strata_sex[order(strata_sex$STRATA),]
radiator::summary_strata(strata_sex)
# Number of strata: 3
# Number of individuals: 109
#
# Number of ind/strata:
# M = 44
# F = 64
# U = 1
#
# Number of duplicate id: 0I then ran sexy_markers as follows with a vcf file available for download from here, and which was checked as follows:
detect_genomic_format(data = "3_subarea_p3_p1r0.6_populations.snps.vcf")
# [1] "vcf.file"
dm_sex <- radiator::sexy_markers(data = "3_subarea_p3_p1r0.6_populations.snps.vcf",
strata = strata_sex)
I am happy to provide further information as needed. Thanks in advance for your help! The R session info is below.
sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] radiator_1.2.5 adegenet_2.1.9 ade4_1.7-20
loaded via a namespace (and not attached):
[1] pkgload_1.3.2 bit64_4.0.5 vroom_1.6.1 splines_4.2.2 shiny_1.7.4 assertthat_0.2.1
[7] BiocManager_1.30.19 remotes_2.4.2 sessioninfo_1.2.2 pillar_1.8.1 lattice_0.20-45 glue_1.6.2
[13] digest_0.6.31 promises_1.2.0.1 colorspace_2.1-0 htmltools_0.5.4 httpuv_1.6.8 Matrix_1.5-3
[19] plyr_1.8.8 pkgconfig_2.0.3 devtools_2.4.5 purrr_1.0.1 xtable_1.8-4 scales_1.2.1
[25] processx_3.8.0 later_1.3.0 tzdb_0.3.0 tibble_3.1.8 mgcv_1.8-41 generics_0.1.3
[31] ggplot2_3.4.0 usethis_2.1.6 ellipsis_0.3.2 withr_2.5.0 cachem_1.0.6 cli_3.6.0
[37] magrittr_2.0.3 crayon_1.5.2 mime_0.12 memoise_2.0.1 ps_1.7.2 fs_1.6.0
[43] fansi_1.0.4 nlme_3.1-161 MASS_7.3-58.2 pkgbuild_1.4.0 vegan_2.6-4 profvis_0.3.7
[49] tools_4.2.2 prettyunits_1.1.1 hms_1.1.2 lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0
[55] cluster_2.1.4 callr_3.7.3 compiler_4.2.2 rlang_1.0.6 grid_4.2.2 rstudioapi_0.14
[61] htmlwidgets_1.6.1 igraph_1.3.5 miniUI_0.1.1.1 gtable_0.3.1 DBI_1.1.3 reshape2_1.4.4
[67] R6_2.5.1 dplyr_1.0.10 bit_4.0.5 fastmap_1.1.0 seqinr_4.2-23 utf8_1.2.2
[73] permute_0.9-7 readr_2.1.3 ape_5.6-2 stringi_1.7.12 parallel_4.2.2 Rcpp_1.0.10
[79] vctrs_0.5.2 tidyselect_1.2.0 urlchecker_1.0.1
Describe the bug When I run the sexy_markers function interactively, if I answer 'n' (i.e. no) the step asking Do you want to continue filtering using long distance ld ? (y/n):, it returns the following error:
Do you want to continue filtering using long distance ld ? (y/n):nComputation time, overall: 10 sec############################# completed filter_ld ##############################Sex-ratio (F/M): 0.82Error: $ operator is invalid for atomic vectorsTo Reproduce I am running the sexy_markers function interactively. The input is a vcf file produced by vcf tools. I checked that the strata file was read in properly with summary_strata.
Steps 1. command sexy_markers(data="path/to/input/vcf.vcf", strata="path/to/input/strata.tsv")
i do not blacklist individual samples i filter short ld with 1 mac when asked if i want to continue filtering using long distance ld, I answer "n" error message below is returned 2. complete error message Error: $ operator is invalid for atomic vectors 3. devtools::session_info() ─ Session info ───────────────────────────────────────────────────────────────────────────────────────── setting value
version R version 4.0.3 (2020-10-10) os macOS High Sierra 10.13.6
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_AU.UTF-8
ctype en_AU.UTF-8
tz Australia/Brisbane
date 2021-02-04
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────── package version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2)
BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor
Biostrings 2.56.0 2020-04-27 [1] Bioconductor
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.2)
callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.2)
cli 2.1.0 2020-10-12 [1] CRAN (R 4.0.2)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2)
conquer 1.0.2 2020-08-27 [1] CRAN (R 4.0.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.1)
data.table 1.13.0 2020-07-24 [1] CRAN (R 4.0.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)
devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
digest 0.6.26 2020-10-17 [1] CRAN (R 4.0.3)
dplyr 1.0.2 2020-08-18 [1] CRAN (R 4.0.2)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
gdsfmt 1.24.1 2020-06-16 [1] Bioconductor
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2)
GenomeInfoDb 1.24.2 2020-06-15 [1] Bioconductor
GenomeInfoDbData 1.2.3 2020-10-19 [1] Bioconductor
GenomicRanges 1.40.0 2020-04-27 [1] Bioconductor
ggplot2 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.2)
htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
IRanges 2.22.2 2020-05-21 [1] Bioconductor
knitr 1.30 2020-09-22 [1] CRAN (R 4.0.2)
labeling 0.3 2014-08-23 [1] CRAN (R 4.0.2)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.3)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.3)
MatrixModels 0.4-1 2015-08-22 [1] CRAN (R 4.0.2)
matrixStats 0.57.0 2020-09-25 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2)
ps 1.4.0 2020-10-07 [1] CRAN (R 4.0.2)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
quantreg 5.74 2020-10-18 [1] CRAN (R 4.0.2)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)
radiator 1.1.9 2021-02-04 [1] Github (thierrygosselin/radiator@5c6b865) Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
RCurl 1.98-1.2 2020-04-18 [1] CRAN (R 4.0.2)
readr 1.4.0 2020-10-05 [1] CRAN (R 4.0.2)
remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
rlang 0.4.8 2020-10-08 [1] CRAN (R 4.0.2)
rmarkdown 2.4 2020-09-30 [1] CRAN (R 4.0.3)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2)
S4Vectors 0.26.1 2020-05-16 [1] Bioconductor
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
SeqArray 1.28.1 2020-06-16 [1] Bioconductor
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
SparseM 1.78 2019-12-13 [1] CRAN (R 4.0.2)
stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2)
tibble 3.0.4 2020-10-12 [1] CRAN (R 4.0.2)
tidyr 1.1.2 2020-08-27 [1] CRAN (R 4.0.2)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2)
tinytex 0.26 2020-09-22 [1] CRAN (R 4.0.2)
usethis 1.6.3 2020-09-17 [1] CRAN (R 4.0.2)
vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2)
withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2)
xfun 0.18 2020-09-29 [1] CRAN (R 4.0.2)
XVector 0.28.0 2020-04-27 [1] Bioconductor
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2)
zlibbioc 1.34.0 2020-04-27 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
4. sample data example.vcf.zip