pgainsim: an R-package to assess the mode of inheritance for quantitative trait loci in GWAS

Scherer, Nora; Sekula, Peggy; Pfaffelhuber, Peter; Schlosser, Pascal

doi:10.1093/bioinformatics/btab150

Cited by 2 publications

(2 citation statements)

References 5 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, as we were only able to identify 19 distinct morphotypes within our population of n = 24 individuals and could not always reliably determine which morphotype was represented in each video, we are limited to treating flight trajectories recorded from the same birds as independent data points. We analysed the data statistically using R (v. 4.0.3) and R Studio (v. 1.3.1093) with the packages PropCIs [ 26 ] and diptest [ 27 ].…”

Section: Methodsmentioning

confidence: 99%

Brightness cues affect gap negotiation behaviours in zebra finches flying between perches

Borsier,

Sanders,

Taylor

2024

R. Soc. Open Sci.

View full text Add to dashboard Cite

Flying animals have had to evolve robust and effective guidance strategies for dealing with habitat clutter. Birds and insects use optic flow expansion cues to sense and avoid obstacles, but orchid bees have also been shown to use brightness cues during gap negotiation. Such brightness cues might therefore be of general importance in structuring visually guided flight behaviours. To test the hypothesis that brightness cues also affect gap negotiation behaviours in birds, we presented captive zebra finches Taeniopygia guttata with a symmetric or asymmetric background brightness distribution on the other side of a tunnel. The background brightness conditions influenced both the birds’ decision to enter the tunnel aperture, and their flight direction upon exit. Zebra finches were more likely to initiate flight through the tunnel if they could see a bright background through it; they were also more likely to fly to the bright side upon exiting. We found no evidence of the centring response that would be expected if optic flow cues were balanced bilaterally during gap negotiation. Instead, the birds entered the tunnel by targeting a clearance of approximately one wing length from its near edge. Brightness cues therefore affect how zebra finches structure their flight when negotiating gaps in enclosed environments.

show abstract

Section: Methodsmentioning

confidence: 99%

Brightness cues affect gap negotiation behaviours in zebra finches flying between perches

Borsier,

Sanders,

Taylor

2024

R. Soc. Open Sci.

View full text Add to dashboard Cite

show abstract

“…Similarly, the false positive rate is defined as the proportion of times we detected at least one false positive per replication out of 100 replications. True and false positive detection rates were further scrutinized by calculating 95% confidence intervals using the method of the Clopper and Pearson (1934) in the PropCIs R package (Scherer and Scherer 2018). For each setting, all SNPs selected to be vQTNs were removed prior to calculating the true and false positive detection rates.…”

Section: Qtn Detection Rates For Competing Modelsmentioning

confidence: 99%

Assessment of two statistical approaches for variance genome-wide association studies in plants

et al. 2022

View full text Add to dashboard Cite

Genomic loci that control the variance of agronomically important traits are increasingly important due to the profusion of unpredictable environments arising from climate change. The ability to identify such variance-controlling loci in association studies will be critical for future breeding efforts. Two statistical approaches that have already been used in the variance genome-wide association study (vGWAS) paradigm are the Brown-Forsythe test (BFT) and the double generalized linear model (DGLM). To ensure that these approaches are deployed as effectively as possible, it is critical to study the factors that influence their ability to identify variance-controlling loci. We used genome-wide marker data in maize (Zea mays L.) and Arabidopsis thaliana to simulate traits controlled by epistasis, genotype by environment (GxE) interactions, and variance quantitative trait nucleotides (vQTNs). We then quantified true and false positive detection rates of the BFT and DGLM across all simulated traits. We also conducted a vGWAS using both the BFT and DGLM on plant height in a maize diversity panel. The observed true positive detection rates at the maximum sample size considered (N = 2815) suggest that both of these vGWAS approaches are capable of identifying epistasis and GxE for sufficiently large sample sizes. We also noted that the DGLM decisively outperformed the BFT for simulated traits controlled by vQTNs at sample sizes of N = 500. Although we conclude that there are still certain aspects of vGWAS approaches that need further refinement, this study suggests that the BFT and DGLM are capable of identifying variance-controlling loci in current state-of-the-art plant or agronomic data sets.

show abstract

pgainsim: an R-package to assess the mode of inheritance for quantitative trait loci in GWAS

Cited by 2 publications

References 5 publications

Brightness cues affect gap negotiation behaviours in zebra finches flying between perches

Brightness cues affect gap negotiation behaviours in zebra finches flying between perches

Assessment of two statistical approaches for variance genome-wide association studies in plants

Contact Info

Product

Resources

About