Questions tagged [genetics]

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

Genetics is the study of genes — what they are, what they do, and how they work. Genes inside the nucleus of a cell are strung together in such a way that the sequence carries information: that information determines how living organisms inherit various features (phenotypic traits). For example, offspring produced by sexual reproduction usually look similar to each of their parents because they have inherited some of each of their parents' genes. Genetics identifies which features are inherited, and explains how these features pass from generation to generation. In addition to inheritance, genetics studies how genes are turned on and off to control what substances are made in a cell-gene expression.

Nowadays, the genetics is interesting in computer science too. It can propose own advances and results of the investigations to describe the information interpretation for very complex objects and needed methods on the algorithmic level. For example, one gene can save value about one feature of the object, furthermore, using different methods of information coding we can expand properties of one gene whereby different shades. Also, considering gene on the abstract level of our understanding, we can build a very powerful system of equations which will be describing the object completely from different aspects.

To know more.

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Plotting gene expression data with means in a randomized experiment

I'm (a newbie to R) analyzing a randomized study on the effect of two treatments on gene expression. We evaluated 5 different genes at baseline and after 1 year. The gene fold is calculated as the value at 1 year divided by the baseline…
Adam Robinsson
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Computing the probability of an offspring having at least one dominant allele

I am trying to solve the 'Mendel's First Law' problem on http://rosalind.info/ I have tried several different approaches, but I just can't get my solution to return the same answer as the sample problem on their page. I know their sample output is…
user3468950
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What is an alternative to leap() that can handle NAs?

Need to apply Branch and bound method to choose best model. leaps() from leaps package works well, only if the data has no NA values, otherwise throws an error: #dummy data x<-matrix(rnorm(100),ncol=4) #convert to 0,1,2 - this is a genetic data,…
zx8754
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Create probability matrices with SNP allele data for ACGT

Given the following data for 8 samples (A1-A8): A1 A2 A3 A4 A5 A6 A7 A8 T T T T T T T C T C T T T T T C A A A G G A A A Where each column is one sample, and each row is one marker with the possible codings A, C, G, T, I wish to calculate the…
user2895292
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R WGCNA Cytoscape hub genes

I have the following problem with WGCNA - http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/ Working on Section 1.6, Export of networks to external software (Cytoscape) I'm currently trying to perform WGCNA…
Derek
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Population genetics modelling in python

so I need to make a program that generates generations of random equally fit alleles of a theoretical organism with a single gene. I start with a list containing one mutated allele 2, and then I choose 3 alleles for the next generation, and append…
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How can I select human miRNA from affy chip while analyzing data using R?

I am new to R and want to analyze miRNA expression from a data set of 3 groups. Can anyone help me out. In this case I got other miRNAs(on affy chips) as top expressed genes. Now I want to select only human miRNAs. Please help me Thanks in advance
Shafi
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random mutation in a DNA sequence - mutation rate in python

EDITED I created a function that introduces random mutations with a determined mutation rate (example 0.05). input='ATCTAGGAT' def mutate_v2(sequence, mutation_rate): dna_list = list(sequence) for i in range(len(sequence)): r =…
user8769986
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How did using a pedigree influence the degrees of freedom available to test fixed effects in asreml-R?

I am using a half-sibling pedigree (individuals, Sires, Dams and groups (populations) assigned). When I run the model I received the message “Terms with zero df listed …” and when I ask for the wald test of fixed effect one of my effects is missing.…
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Probability estimates from Google AutoML

I am analyzing pedigrees to determine if families have a cancer susceptibility gene mutation based on their family history of cancer (various types). I have created a dataset for Google AutoML Tables with 250,000 generated pedigrees. I would like to…
Ian Grady
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Remove unnecessary information from SNP rsid names

I have a dataset of SNPs, which aren't coded the way I need them. Instead of being coded just "rsNUMBER" they also have the information of the chip-analyses. For example: GSA-rsNUMBER or psy-rsNUMBER Some also have the information of the…
Inken
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Most efficient way to run regression models for multiple independent variables on the same list of 80 dependent outcomes?

What is the most efficient way to run regression models for a list of 20 independent variables (e.g. genetic variants, each of these genetic variants will be tested alone) and 40 dependent variables? I am a beginner to R! I found a solution but it…
rkl
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DNA sequence Dotplots

I'm currently writing a script to create a Dotplot when two sequences are given. So far I can get a lovely lil dotplot. The X axis is: >HeaderOfSeq1 X = ATCGTAGCTACGTACGT The Y axis is: >HeaderOfSeq2 Y = ATGCGATCGTGCTAC…
DLBPointon
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Extracting values from matchPattern

I am using matchPattern function from Biostrings package to find particular sequences in the genome. Once found, I want to show and frequency distribution of the spacing between the matched instances. Example: running the following code Match1 <-…
FranjoIM
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Cannot cast Comparable to a class which implements it

I'm trying to create a genetic ArrayList of my class Team but I can't cast Comparable to T despite that T extends Comparable (I tried extends Comparable without putting < T > and same problem is happening) public class ArrayList
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