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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Is there a way to collapse and convert a dataframe based upon multiple criteria?

I have a dataset (matrix) of genotypes at different marker loci. structure(list(Genotype = 1:5, Locus_1a = c(0L, 1L, 1L, 1L, 1L ), Locus_1b = c(1L, 1L, 0L, 1L, 0L), Locus_1c = c(1L, 0L, 1L, 1L, 0L), Locus_2a = c(0L, 1L, 1L, 0L, 0L), Locus_2b = c(1L,…
Josh
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How can I extract trailing garbage from a gzipped vcf file?

I cannot extract all of the contents of a gzipped vcf file. The file is part of an encrypted tarball I downloaded from dbGaP. After decryption, I was able to extract a directory of files with this command: tar -xvf phg001.tar When I used Plink…
PaulJ2.0
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How to update an RData file that was generated using older version of R and its packages to a current version of R?

Hello my fellow R community, I have an ".RData" file, generated by someone somewhere between 2014-2016. This was related to Differential Expression Analysis for his previous RNASeq project. Loading this file into R produces a number of objects that…
BS7-ESR10
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Warning message using SNPassoc package

I'm using SNPassoc R package for finding association between data SNPs and a binary variable outcome. This is the model: model <- WGassociation (continuous variable ~ covariate +covariate+ covariate ,data= data) model I run the analysis and I got…
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R code for paired permutation t-test in a loop

I have some genetic data, which looks…
EmmaH
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How to shade custom blocks in Circlize package in R

I am using the R package circlize to create a circos plot. I am aiming to create something similar to Figure 2 in this paper: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004812. I would like to custom specify where to…
Will Hamilton
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Creating maps with pie charts from genetic data

I am doing a population genetics study and working with chloroplast data from an oak species. I have performed a DAPC and found that there are 5 clusters of chloroplast genotypes. I want to make a map that shows the ratios of each of these based on…
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how to convert imputed dosage files to plink format files

I am trying to convert imputed dosage file from michigan imputation server to plink files. For this purpuse I am using a tool called dosageconvertor. I tried to install it using the commands: > git clone https://github.com/Santy-8128/DosageConvertor…
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Split multiallelic to biallelic in vcf by plink 1.9 and its variant name

I am trying to use plink1.9 to split multiallelic into biallelic. The input is that 1 chr1:930939:G:A 0 930939 G A 1 chr1:930947:G:A 0 930947 A G 1 chr1:930952:G:A;chr1:930952:G:C 0 930952 A …
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Can analysis of GWAS/WES/WGS be performed with DNA from saliva in combination with DNA from blood?

Can statistical analyses (GWAS/WES/WGS) be performed with DNA from saliva in combination with DNA from blood? Is there a chance of bias? First, I think DNA=DNA, in other words, no matter how the 'DNA code' is collected. But there may be unexpected…
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How do I create a volcano plot using bioinfokit?

I have been trying to use python and bioinfokit to create a volcano plot of gene expression data that's in an excel file. I used pandas to create a data frame and then eliminated some negative values. I then tried to create the volcano plot in the…
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How can I match data from a list to a column from an array?

I am very new to R, and this might be a silly question, but I appreciate any help in advance. I have a large data frame named df_long0 with a column titled Gene.names. I have another matrix titled annotLookup with two columns: gene and ensembl. I…
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Error in rowSums(tbl.external.all) : 'x' must be numeric

I try to run SKAT derived R tool, but get stuck with some bug in it. When running almost last step of the script re<-iECAT.SSD.All(EC.INFO, obj=obj, method="optimal") I get following error: Error in rowSums(tbl.external.all) : 'x' must be…
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Removing only part of character line in txt file - chr string

I would like to remove strings "chr" in a following txt file, using bash: FO538757.1 chr1:183937 AL669831.3 chr1:601436 AL669831.3 chr1:601667 AL669831.3 chr1:609395 AL669831.3 chr1:609407 AL669831.3 …
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What does my "Error: factor level [4] is duplicated" in AS-Reml R mean?

For my PhD I am currently running a bivariate variance component estimation in AS Reml R with the following command: Test <- asreml(cbind(Reflex,lakt_1) ~ trait + Betriebsnummer + at(trait,1):gestLength + at(trait,1):halfyear, random=…