Tag: qqplot

CIMB | Free Full-Text | mtDNA Single-Nucleotide Variants Associated with Type 2 Diabetes

1. Introduction Type 2 diabetes (T2D) is the most prevalent metabolic disease and a significant public health concern [1,2], leading to early-onset disability and elevated mortality due to various related complications [3]. Between 1990 and 2017, the global trend in the age-standardized rates of T2D, as measured by the number…

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Skewed qq plot from logistic regression

I have two cohorts (of differing sizes, one ~2300 and one ~130 people) and have calculated logistic models of the presence/absence of a genetic mutation between the two groups (corrected for some nuisance factors): Variant ~ Cohort + other where Variant is a binary variable (whether the variant is present…

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smallRNA-seq analysis batch correction in limma

Good morning, I am currently trying to analyse a small-RNA sequencing dataset using limma package and the voomLmFit function. However, I am experiencing some issues with the p-value distribution, with some of the comparisons I am testing showing odd p-value distribution. This probably indicates that there is some kind of…

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bcftools to R for fst by distance coding issue

Im having an issue with code or perhaps the file. The code is below and the error that I got was“Error in file(file, “r”) : cannot open the connection In addition: Warning messages: 1: In file2other(input, type, match.arg(type.out), match.arg(allele.sep)) : Converter vcf to pcadapt is deprecated. Please use PLINK for…

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ggplot2 – R, Name of Scales

I am try to make qqplot with R, but something changed the column name and I canĀ“t figure out what exactly. This is code : ggplot(aggMW, aes(x = factor(State, levels = c(“silent”, “steady”, “changing”)), y = NoCorrect, fill = OnSpeaks)) + geom_bar(stat = “identity”, position = “dodge”) + facet_grid(Group ~…

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coef /makeContrasts very different results

I have a situation where I have a factoral independant variable ‘suicide’ with three levels ‘non_suicide’, suicide, and ‘unkown’. I have been setting up my analysis thus: suicide.non.undet <- as.factor(df$suicide) CauseofDeath.recode <- as.factor(df$CauseofDeath) Sex <- as.factor(df$Sex) Smoking <- as.factor(df$Smoking) Ethanol <- as.factor(df$Ethanol) svseq1 <- as.numeric(df$svseq1) design1 <- model.matrix(~ suicide +…

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python – Getting AIC of lognormal distributions using scikit’s GMM

The short answer is that you should not compare aic of models that have different scales of response variables. See post like this or this. So for example you can compare gmm = GaussianMixture(n_components = 1).fit(X=np.expand_dims(data,1)) print(gmm.aic(X=np.expand_dims(data,1))) gmm2 = GaussianMixture(n_components = 2).fit(X=np.expand_dims(data,1)) print(gmm2.aic(X=np.expand_dims(data,1))) 18753.718210403502 17498.87614003799 You can see that the…

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How to make Q-Q plots for different models at a single chart using R?

How to make Q-Q plots for different models at a single chart using R? 1 Hello everyone! I am trying to make a Q-Q plot to visualise p-values obtained from different models afterr runing GWAS analysis. The key thing is that I want to reflect p-values from the different models…

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Cool Bioinformatics Scripts With Python

You can use this script in two ways read tons of millions of P values from stdin # python zcat pval.txt.gz | qqplot.py -out test -title “QQ plot on the fly” # julia zcat pval.txt.gz | qqplot.jl –out test –title “QQ plot on the fly” warning : If you have…

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GitHub – Zilong-Li/BioScripts: Cool Bioinformatics Scripts

You can use make a QQ plot in the following ways. one-liner for reading tons of millions of P values from the pipe # python zcat pval.txt.gz | qqplot.py -out test -title “QQ plot on the fly” # julia (recommand to run it in the REPL) zcat pval.txt.gz | qqplot.jl…

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Cool Bioinformatics Scripts | PythonRepo

You can use this script in two ways read tons of millions of P values from stdin # python zcat pval.txt.gz | qqplot.py -out test -title “QQ plot on the fly” # julia zcat pval.txt.gz | qqplot.jl –out test –title “QQ plot on the fly” warning : If you…

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Dealing with P value inflation of SNPs identified by qqplot

Dealing with P value inflation of SNPs identified by qqplot 0 I’m attempting to call SNPs that changed in allele frequency in a population. The population was sequenced at two times (before and after a drought) using pooled-sequencing of the whole genome. Fisher exact tests identified 7 million SNPs, which…

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