Questions tagged [genetics]

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

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14 views

Measuring Co-Occurrence of Data

In this case I am trying to study the co-occurrence between GC pairs in a genome, supporting it both with visualizations (heatmap and networks). Basically I'm trying to find associations (GC pairs ...
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1answer
10 views

PCA clustering and creating a new covariate for RNAseq

I am currently doing an RNAseq experiment and some quality control on data. I noticed that there seems to be some kind of batch effect that I cannot explain from the variables I already have. I've ...
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Is there a way calculate a gradient of dissimilarity across multiple sites using presence/absence data?

I’ve been trying to come up with a metric for species (dis)similarity for fish in a series based on presence or absence data that gives a value of 1 or 0 for each lake. From my research, it seems like ...
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9 views

Calculating heritability from half-sib design

I'm trying to measure heritability of a trait, flowering time (FT), for a set of data collected from a half-sib design. The data includes FT for each mother plant and 2 half siblings from that mother ...
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12 views

Statistical method for estimation of Penetrance

I was thinking on a problem: there is a rare disease, associated with some ultra-rare genomic variant (which means ~ 1 out of millions), and there are estimations of penetrance (how many individuals ...
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1answer
27 views

Categorization of continuous predictor in logistic regression

I have one continuous variable GENETIC SCORE and one binary variable HEALTH (case vs control i.e. 0/1). I want to fit a log regression model to this data to get the odds ratio for different percentile ...
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54 views

Binomial proportion confidence interval when rigid bounds on population proportion (0.5 < p < 1)

A standard problem is estimation of confidence intervals for a population proportion given that one has observed f successes out of n independent trials. There is a reasonable discussion of this ...
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1answer
41 views

What is penetrance and why is a family study needed to estimate it?

In this statistical genetics article, the authors discuss the issue of not knowing the cancer penetrance of a certain gene variant. They say this is because families with disease history are more ...
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1answer
29 views

Statistical significance in mutations in two groups

I'm doing an analysis examining the mutations of a set of ~3 genes in 4 different populations. For Gene 1: In Group A 33/540 have that mutation, Group B 66/100, Group C 15/213, and Group D 20/32. And ...
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1answer
19 views

ATGC sequence of gene expression data [closed]

I am not a pro in genetics so please excuse my non-technical language. I need dataset which contains the gene expression as well as the associated ATGC sequence with each gene expression value. For ...
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21 views

Poisson and Gamma distribution for testing randomness

In genetics I want to test whether InDel (insertion and deletion in DNA) sizes occurs with the same probability. I heard that I should gamma distribution to model it. I found ...
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64 views

How to calculate bootstrap values for Fst?

I want to try to get the significance of my Nei Fst values through bootstrapping. I have a large data set of SNPs from RADseq data. They are in 4 populations: River, Lake, Outgroup1, Outgroup2. My ...
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23 views

How to calculate Fst from multiple loci?

I am having a lot of trouble calculating correct Fst values for my SNPs. Whilst my data doesn't have any population in it, I have added pop as a factor, separating my data into 4 different populations....
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9 views

For a meta-analysis study, is it correct to derive specific haplotypes from multiple studies that report varying number of SNPs at a gene locus?

My question is based on conducting a meta-analysis on the association of multiple variants in a single gene with a complex disorder using published case-control studies. For my study, around 5 well-...
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34 views

Calculating heritability: pedigree information with family variation

currently I am aiming to calculate heritability, for which I would have to estimate additive genetic variance (the inverse of the relatedness matrix) for a first step. This is done with the following ...
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27 views

Appropriate statistics for multivariate genetic analysis

I have a question on the most appropriate statistics for our genetic project. We have a dataset consisting of genotypes at several loci (10 SNPs) and phenotypes (the same person can be a control for ...
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25 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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39 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
141 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
37 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
223 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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67 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
88 views

To find p-value of compounds

I have next SNPs data.frame structure ...
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119 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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24 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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18 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
106 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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180 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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75 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
3k 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
100 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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71 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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86 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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51 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
483 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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29 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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20 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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48 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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77 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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43 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
47 views

Regression Analysis, multivariate analysis

I have a data which looks like this: ...
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1answer
65 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 ...
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2k views

genes significantly different compared to other groups

I am trying to compare genes that differ significantly between groups and only plot them in the heatmap. I am using R and its libraries ComplexHeatmap and cirlize. The sample of the data that I have ...
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1answer
90 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
324 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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455 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
120 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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131 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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64 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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98 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 ...