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thierrygosselin avatar thierrygosselin commented on June 23, 2024

Welcome to GitHub Tina
I'll have a look at this later today
Best
Thierry

from radiator.

thierrygosselin avatar thierrygosselin commented on June 23, 2024

updates....
I'm able to reproduce your error with the provided data...
I'll have a fix

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thierrygosselin avatar thierrygosselin commented on June 23, 2024
test1 <- radiator::read_dart(
  data = "Report_DAci24-8986_2_moreOrders_SNPcount_2_CSedit_working_all_dupsremoved.csv",
  strata= "(5)strata_dart_sturgeon_20240427_mod.tsv"
  )

works

Reading DArT file...
Number of blacklisted samples: 239
DArT SNP format: alleles coverage in 2 Rows counts
fstcore package v0.9.18
(OpenMP detected, using 56 threads)
Generating genotypes and calibrating REF/ALT alleles...
Number of markers recalibrated based on counts of allele read depth: 5398
Generating GDS...
File written: [email protected]

Number of chrom: 1
Number of locus: 28804
Number of SNPs: 33736
Number of strata: 27
Number of individuals: 2525

Number of ind/strata:
  GFR = 417
RAL = 49
RAR = 49
NMW = 5
ENG = 50
CAR = 138
WHD = 19
TET = 56
BOU = 27
PPE = 20
SFC = 88
SFB = 38
SFA = 24
DSS = 92
NUM = 125
NUT = 125
PIG = 2
PFR = 815
DOR = 35
SEM = 24
LDB = 87
DSP = 57
ASS = 30
EBC = 20
CHR = 20
GUL = 69
STE = 44

Number of duplicate id: 0

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thierrygosselin avatar thierrygosselin commented on June 23, 2024
test2 <- radiator::read_dart(
  data = "Report_DAci24-8986_2_moreOrders_SNPcount_2_CSedit_working_all_dupsremoved.csv",
  strata= "(5)strata_dart_sturgeon_20240427_mod.tsv",
  tidy.dart = TRUE
)

works

from radiator.

thierrygosselin avatar thierrygosselin commented on June 23, 2024
test3 <- radiator::filter_rad(
  data = "Report_DAci24-8986_2_moreOrders_SNPcount_2_CSedit_working_all_dupsremoved.csv",
  strata= "(5)strata_dart_sturgeon_20240427_mod.tsv"
)
Generating statistics
✔ Missing genotypes [3.1s]
✔ Heterozygosity [1.5s]
Error in `dplyr::filter()`:
ℹ In argument: `MARKERS %in% markers`.
Caused by error:
! object 'MARKERS' not found
Run `rlang::last_trace()` to see where the error occurred.
✖ Coverage ... [2.9s]

from radiator.

thierrygosselin avatar thierrygosselin commented on June 23, 2024

Version 1.3.2 should work with your dataset

test this:

data <- radiator::filter_rad(
  data = "Report_DAci24-8986_2_moreOrders_SNPcount_2_CSedit_working_all_dupsremoved.csv",
  strata= "(5)strata_dart_sturgeon_20240427_mod.tsv"
)
  • You'll see your duplicates easily, look carefully at those from different groupings, those are id errors or sampling/wet lab problems.
  • Be careful how you handle the juveniles and broods during SNP discovery, they have potential to bias a lot. Looking at the close kin fig will highlight that

Getting this at the end is normal, part of it will be fixed but it doesn't change anything. It's code cosmetic.

############################# completed filter_rad #############################
Warning messages:
1: In ggplot2::scale_y_log10(labels = scales::number_format(), oob = scales::squish_infinite) :
  log-10 transformation introduced infinite values.
2: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `WHITELISTED_MARKERS = purrr::map_int(...)`.
Caused by warning:
! Using one column matrices in `filter()` was deprecated in dplyr
  1.1.0.
ℹ Please use one dimensional logical vectors instead.
ℹ The deprecated feature was likely used in the radiator package.
  Please report the issue at
  <https://github.com/thierrygosselin/radiator/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning
was generated. 
3: Unknown or uninitialised column: `STRATA`. 
4: Unknown or uninitialised column: `STRATA`. 
5: Unknown or uninitialised column: `STRATA`.

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