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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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17 views

Which statistical studies should be carried out for expression analysis of genes when I have fold change data of genes

I am new to R and data analysis. I am working on gene expression. My data frame contains Gene_ID and quantification_value which is the fold change of the gene. ( the value represents the amount by ...
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2answers
51 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
38 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
25 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
16 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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0answers
18 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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42 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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14 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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0answers
24 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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25 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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17 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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35 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
133 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 ...
9
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1answer
194 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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64 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 ...
3
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0answers
117 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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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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17 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
102 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
128 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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65 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. ...
3
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2answers
2k 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
93 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)...
2
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0answers
62 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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0answers
83 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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49 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 ...
3
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2answers
463 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
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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19 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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0answers
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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0answers
74 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 ...
2
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0answers
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
45 views

Regression Analysis, multivariate analysis

I have a data which looks like this: ...
0
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1answer
60 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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0answers
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 ...
2
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1answer
70 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 ...
0
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1answer
274 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
415 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 ...
1
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1answer
112 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
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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0answers
63 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 (...
4
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2answers
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 ...
1
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1answer
33 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 ...
1
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1answer
182 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
87 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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336 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 ...