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Questions tagged [genetics]

The scientific study of the principles of heredity and the variation of inherited traits among related organisms.

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3 views

Nested ANOVA (half sibling design) using binomial data?

Short question: I was wondering what kind of nested ANOVA-style analyses are available for binomial data? I would like to specifically compare the variances between Level A groups, but also between ...
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28 views

How should I interpret a weighted genetic risk score?

I created a weighted Genetic Risk Score (GRS) by summing the product of the SNP-dosages times their regression coefficients from the GWAS in which I found them. So: ...
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1answer
116 views

Linear Regression Approach For Trends

I'm working on a project with genetics but I think my problem is applicable to general statistics. I want to test frequency (Minor Allele Frequency) of a SNP/variant across 5 age categories to see ...
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1answer
32 views

A question about pca and gene function analysis

I'm new to bioinformatics, and I have a pretty basic question. Let's say I have a bunch of genes {Xi} and I want to know which one has the most significant on some measurable phenotypic trait Y. Now I ...
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1answer
170 views

How do children manage to pull their parents together in a PCA projection of a GWAS data set?

Take 20 random points in a 10,000-dimensional space with each coordinate iid from $\mathcal N(0,1)$. Split them into 10 pairs ("couples") and add the average of each pair ("a child") to the dataset. ...
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40 views

Interpreting PCA, comparing genetic structure within mice population from two continents

I'm interested in comparing the intra-regional genetic relatedness between two populations of mice. One population is native to Europe, while the other is native to North America. I ran PCA to find ...
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1answer
85 views

To find p-value of compounds

I have next SNPs data.frame structure ...
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25 views

Pairwise comparison for differences between Coefficient of Variation Ranking between groups

I would like to test whether the ranking obtained by ordering the coefficient of variation of some genes are different or not between two groups, and do it pairwise, so, row by row, and get a p-value ...
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34 views

Power of an association study / GWAS

I came across this chunk of text in this paper: The power of association studies is dependent on the variance explained by a locus; thus, for a disease that affects 1% of the population, we ...
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14 views

Proportion of a gene mutation across different age groups

I am trying to analyze in SPSS if there a significant difference in the proportion of a gene mutation among different age groups (20-29, 30-39, etc). I codified the age groups from the continuous var ...
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0answers
112 views

Correcting for noise in gene expression data

I have a training set of RT-qPCR gene expression data (not run in triplicate) for a batch of samples with two phenotypes $A$ and $B$ on which I've trained a logistic regression classifier. I also ...
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0answers
23 views

Is it wrong to standardise a variable and then centre it for use in multiple regression? [duplicate]

Is it wrong to standardise a variable (e.g. polygenic risk score) and then centre it for use in multiple regression?
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0answers
16 views

Avoiding pairwise analysis in count data?

I'm having some trouble choosing an appropriate analysis method for some count data that I have. I'm looking at mutation counts in 50 genes across 6 related disease states. Counts range from 0 to ~400 ...
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1answer
84 views

Population stratification: adjustment via principal components analysis

I'm new to statistical genetics and trying to learn more about using principal components to adjust for population stratification in case-control studies. My understanding is that the PCA approach ...
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0answers
19 views

Comparing theoretical and experimental percentages of base frequency

I have the theoretical percentage and experimental percentage for 7 genome mutations. I want to compare the experimental and theoretical values to gain a p-value. I am using GraphPad Prism so am ...
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0answers
81 views

How to Solve this Conditional Probability Problem? Probability of Twins

I'm working on a problem from a textbook (self-study) (Casella and Berger). The Problem Given these facts/assumptions... ⅓ of human twins are identical (one-egg) and ⅔ are fraternal (two-egg). ...
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53 views

Heritability estimation for germination success

I am estimating heritabilities for some traits using a parent-offspring regression in R. For mid-parents this means that the regression coefficient of a linear model is equal to the heritablility. ...
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2answers
1k views

Calculate heritability from an anova result

QUESTION Is it possible to extrapolate the heritability from an ANOVA result? POSITIONING THE PROBLEM Heritability is an indicator specific of a phenotype and a an experiment. It is usually calculate ...
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1answer
79 views

Deconvolution methods in biostatistics [closed]

I am currently in a Biostatistics project using deconvolution methods (i.e. Cybersort, link provided below). However I have very limited background on biology (merely 1/3 of an intro to biology course)...
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0answers
52 views

Any R packages that can perform generalized linear mixed model with Firth correction? [closed]

I am performing a genetic association analysis with binary outcomes (case-control study) and would like to include a genetic relatedness matrix (GRM or kinship matrix) as a covariate along with others....
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63 views

StringTie - Transcript matching to multiple genes

I am trying to analyse differential gene expression in 83 samples split up into three groups following the protocol described by Pertea et al., 2016 (doi:10.1038/nprot.2016.095). Now I have two CSV ...
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46 views

Question regarding multiple random forest or gradient boosting models for identification of strong predictor

I have worked in R previously but I'm quite new to predictive modeling with Random Forest and Gradient boosting models in R. I have a dataset with 100 healthy individuals and 50% of the dataset has ...
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2answers
434 views

Does having your first child not be color-blind change the odds that the next ones will be?

I'm graduated now, and swear I remember this exact kind of problem coming up in my Bayesian statistics class, but I can't remember what the answer was. The Problem So my wife's brother is red/green ...
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0answers
26 views

Distribution of chromosomes in sample of sperm cells

Presumably in an ejaculation sample from a human, each sperm cell contains half of the chromosomes from a full cell. Hence every chromosome is equally present in the cells of a sperm sample. However, ...
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18 views

Likelihood of pathogenicity

Suppose that the probability that a mutation in a bacterium is pathogenic is 1/100. Now, a new allele is found in a population with a frequency of 5%. What is the probability that this mutation is ...
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44 views

Modelling approach for large data set with many small clusters and rare outcome

Hi, I am trying to find out whether a certain behavioral trait in birds is heritable and have ~ 10K 3-generation pedigrees of birds (N total birds ~ 200K). Not all pedigrees have 3 generations of data-...
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0answers
71 views

Can I use the eigenvectors of a principal component for gene discovery?

I am working on a microarray dataset with n samples x m genes, with metadata including a grouping of interest and other summary statistics, e.g. age, bmi. My objective is to find genes that may be ...
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0answers
38 views

How to analyse GWAS data of co-morbid disorders?

Lets say I am running a GWAS for a disease condition O , where all my cases has one or more of the following diseases: A, B, and C, in addition to my outcome of interest O. So I include individuals ...
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1answer
42 views

Regression Analysis, multivariate analysis

I have a data which looks like this: ...
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1answer
49 views

SNP data, control for sibling effect?

I have some SNP data, and wanted to investigate the association between mother's SNPs and a phenotype in their children. In my model, the child's phenotype is the response variable; mother's SNP is ...
2
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1answer
59 views

Probability of a genetic disease in the family after 3 generations?

A person can be free from Cystic Fibrosis, a carrier of a single gene, or have two genes. Those with two genes have the condition (let's assume they can't have children, though that's not strictly ...
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1answer
212 views

Cluster Analysis of Single-Cell Gene Data

I have a dataset of 480 cells (observations) by 57 variables (48 are gene expression levels). Multiple cells (approximately 24) are sampled from within each patient. Therefore, I have have a variable ...
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0answers
321 views

monotonically decreasing probability distribution

I'm interested in modelling a process where, given $x_{1}<x_{2}$, then $P(x_{1})>P(x_{2})$, with $P(x)$ representing the density of the distribution at $x$. I know that the Exponential ...
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1answer
105 views

What is the interpretation of an S-shaped curve in the plot of eigenvalues of covariance matrix

From PCA's point of view, eigenvalues of covariance matrix should correspond to the principle components. Therefore, when we plot these eigenvalues on a data sets with some clustering pattern, we ...
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0answers
130 views

Have I chosen the right model for the analysis?

What kind of data I have? I have *.csv file with the following structure: ...
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0answers
61 views

Ordinal logistic regression for allele frequencies?

I have some data I would like to look at to investigate associations between specific TLR genotypes (wild type, heterozygous, homozygous) and both a binary outcome variable (death) and continues (...
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2answers
85 views

Inferring alleles distribution from the blood types distribution

The blood type distribution in the US is as follows (according to this link): O 45% A 40% B 11% AB 4% However the blood type is a result of the 2 alleles (in ...
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1answer
31 views

Statistical Power depending on Level of Measurement

It is intuitively clear that a statistical analysis based on continuous data is more informative (i.e. has more statistical power) than if the same data is transformed into a categorical variable ...
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1answer
138 views

What are some good resources to learn Statistical Genetics?

I have a B.S. and M.S. degree in Statistics. I have experience in R. I know the basic structures of Python [Expertise Level: Beginner]. I would really appreciate if you can share with me some ...
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0answers
70 views

Sampling pairs without replacement from two urns with overlapping populations

I have been trying to derive the coefficient of inbreeding lately, but I am at a loss. If I understand correctly it measures the probability of an allele "collision" i.e. getting the same allele from ...
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0answers
24 views

What is an appropriate measure of determination in genetic studies?

Main Question What is an appropriate measure of determination in genetic studies? I used to think that $R^2$ was such a measure, but I'm no longer so sure. Specifically, it seems that $R^2$ ...
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24 views

How do we optimize a given set of features using genetic algorithms for prediction such that we are able to forecast the output?

We traditionally use machine learning and pattern recognition techniques to make forecasts and predictions. However, we wish to test how well Genetic Algorithms or Evolutionary approaches would do in ...
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263 views

Why does the heatmap of this gene expression data don't show a decent clustering here?

The heatmap has samples in columns and probesets/features in the rows. The genes are already selected based on a very low p-value threshold using 2 sample t-test on the two phenotypic subgroups of the ...
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0answers
31 views

Trying to understand variance components methods in quantitative genetics

As described here, the variance components approach to quantitative genetic analysis assumes a mixed linear model, $$ \textbf{y}=\textbf{X}\beta{}+\textbf{g}+\textbf{e}\textrm{,} $$where $\textbf{y}$ ...
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0answers
141 views

How to interpret data spread across diagonal lines in a PCA plot?

On occasion, I'll construct a PCA plot and find that instead of data spreading across PC1 or PC2, it appears to spread across some diagonal line(s) in the plot. For example, in this article on human ...
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0answers
51 views

SCDE inference methods: traditional Bayesian statistics or something else?

This question is about SCDE: http://hms-dbmi.github.io/scde/ Specifically, it is about the third equation on page 5 of the SCDE paper, which reads $$p_S(x) = E\left[\prod_{c\in B} p(x|r_c, \Omega_c)...
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1answer
13 views

Differential Expresion Comparisons

In a Differential expression experiment concerning a gene of interest there is an upregulated condition, downregulated condition and control. When comparing these, it obviously makes sense to compare ...
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0answers
53 views

Identify differentially expressed genes across genotypes

I have 40 different genotypes of rice. For each genotype, I have two replicates under control treatment and two replicates under drought treatment. We sequenced those samples and get read counts of ...
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0answers
258 views

What is the null distribution of the between-group variance?

Scenario From a population, we randomly sample $n$ individuals, measure the normally distributed random variable $X$ and compute the total variance $V_T$ of $X$ in this sample. Then, we randomly ...
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89 views

Interpreting PCA results on gene expression data

I'm working on a gene expression dataset from patients who either have systemic sclerosis or not. I normalized the data with housekeeping gene values and scaled the expression values for each DNA ...