gl.report.parent.offspring
Alan Couch
devtools::install_github("green-striped-gecko/dartR.base@dev")
Peter Unmack
You are probably working on an old file from DArT which has the correct
column for RepAve, but with a different name, probably
AvgReproducibility or something like that. Just rename that column in
your data file and it will work. It's usually the last column before
the actual genotype calls by individuals. Failing that, just add a
column, make all the values 1 and call it RepAvg.
We've got a lot of stuff going on with cods these days in case you are
interesting, whole genomes and all kinds of fun stuff. Hope you are
doing well these days.
Cheers
Peter
On 12/05/2025 6:38 am, Alan Couch wrote:
> Since gl.join was fixed in the dev release recently (thanks Luis!):
>
> # Install developing version of dartR.base
> devtools::install_github("green-striped-gecko/dartR.base@dev")
>
> gl.report.parent.offspring coincidentally is giving me the following error:
>
>> po<-gl.report.parent.offspring(gl) Starting gl.report.parent.offspring
> distribution of counts ofpedigree incompatibilityDataset does not
> include RepAvg among the locus metrics,therefore the reproducibility
> filter was not usedError in 1:nLoc(x) : NA/NaN argument
> I have filtered:
>> gl.filterallna(gl)
>> gl.report.allna(gl) Starting gl.report.allna Identifying loci and individuals scored all
>
> Wondering if I have made a mistake or if we have broken something in the
> gl along the way?
>
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Alan Couch
MarkerName
AlleleSequenceAlt
Variant
CallRate
OneRatioRef
OneRatioSnp
FreqHomRef
FreqHomSnp
FreqHets
PICRef
PICSnp
AvgPIC
AvgCountRef
AvgCountSnp
RatioAvgCountRefAvgCountSnp
Jose Luis Mijangos
Hi Alan,
The issue you're encountering is due to some missing values in the slot where rdepth values are stored. We're working on a more general fix, but in the meantime, you can resolve it by assigning a value to the missing entries—here’s a quick workaround:
library(dartRverse)Also, just a quick note about gl.join: it's mainly intended for joining very large datasets, like the kind DArT often delivers in two separate files. If you're trying to join datasets from different orders, there could be issues—like each dataset having a different reference allele—that might bias your analyses. In those cases, we recommend asking DArT to co-analyse the orders (i.e., re-call genotypes from both orders together).
Cheers,
Luis
Alan Couch
Bernd.Gruber
Hi Alan,
It is possible to “recall” also yourself if that is the only issue, but as luis wrote better to ask dart if possible as they can then also standardise the other loc metrics which are not necessarily to be recalculated. E.g. reproducibility
From: da...@googlegroups.com <da...@googlegroups.com>
On Behalf Of Alan Couch
Sent: Tuesday, 13 May 2025 9:22 AM
To: dartR <da...@googlegroups.com>
Subject: Re: [dartR] gl.report.parent.offspring
Super helpful. Thanks so much. Special thanks for the tip where I might be joining with some risk! I will discuss with Andrzej.
On Tuesday, 13 May 2025 at 09:04:37 UTC+10 luis.m...@gmail.com wrote:
Hi Alan,
The issue you're encountering is due to some missing values in the slot where rdepth values are stored. We're working on a more general fix, but in the meantime, you can resolve it by assigning a value to the missing entries—here’s a quick workaround:
library(dartRverse)
t1 <- readRDS("gl.rds")
# Identify NAs
na_loc <- which(is.na(t1$other$loc.metrics$rdepth))
# Replace NAs with the mean rdepth
t1$other$loc.metrics$rdepth[na_loc] <- mean(t1$other$loc.metrics$rdepth, na.rm = TRUE)
r1 <- gl.report.parent.offspring(t1)
Also, just a quick note about gl.join: it's mainly intended for joining very large datasets, like the kind DArT often delivers in two separate files. If you're trying to join datasets from different orders, there could be issues—like each dataset having a different reference allele—that might bias your analyses. In those cases, we recommend asking DArT to co-analyse the orders (i.e., re-call genotypes from both orders together).
Cheers,
Luis
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