Comments (6)
Welcome to GitHub Tina
I'll have a look at this later today
Best
Thierry
from radiator.
updates....
I'm able to reproduce your error with the provided data...
I'll have a fix
from radiator.
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
from radiator.
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.
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.
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`.
from radiator.
Related Issues (20)
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