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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Print and combine contents from cell if other value of other cell is true

Been trying to figure this out for a while, hoping someone might have an idea or has come across something similar. I currently have an excel sheet that shows a genetic sequence in Row 2 split into three letter codons within a cell which has a…
Chris H
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How to modify the SNP values?

My dataset has 3 SNPs which looks like below Id SNP1 SNP 2 SNP3 1 AA AA AA 2 AG AC AG 3 GG CC GG 4 5 6 So on In SNP1 - I would like to modify the values AA =2, AG =1, GG = 0 and Likewise in SNP1 and SNP2 How…
Mahan
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How to use the content of a list of objects as a condition for a loop to modify a dataframe in python

Here is my question. I have a "list" of objects and a data frame as heads below: 0 0 hsa-let-7f-2-3p 1 hsa-let-7f-2-5p 2 hsa-miR-105-3p 3 hsa-miR-105-5p 6 hsa-miR-106a-3p And Gene_ID miRNA_family_ID 1452449 …
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Data stucture for large binary data manipulation

Hello fellow programmers, I am working on a genetic project where the speed efficiency is crucial. I have essentially a lot of binary data to process. I work in c++11. I have two functions that needs to be optimized. First, I need to be able to use…
Eric
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How to pass a String parameter to a void method?

I need to write a Java program for a course I'm taking which looks for genes in a strand of DNA.The Issue I am having is that from the test method, I need to pass printAllgenes(a) to the void printAllgenes method. In the test method I've tried…
Ryan
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Matching legend to plot points in R Manhattan Plots

I am creating a Manhattan plot in R, where my aim is to highlight SNPs based on the trait they relate to. Here is the tail of my main dataframe (gwas_plot): SNP CHR BP P 58008 rs77855001 1 249213034 8.665e-01 58009 …
IcedCoffee
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Best way to create a Punnett Square in PHP?

I've hunted high and low for some answers to this but can't find anything helpful. I'm working on a genetics project, and I need to create a script that can generate a punnett square from the genetics passed. The sort of thing I'll be working with…
Andy Holmes
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Mapping CpG Coordinate using a .bam file

I found a way to map the CpG position on the chicken genome, as follows: library(BSgenome.Ggallus.UCSC.galGal4) library(Biostrings) #Create the chromossome set chr_all=paste("chr", c(1:28, 32, "Z", "W"), sep="") #CpG Mapping on Genome …
Fpertille
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How can I retrieve gene annotation info (more specific - functions) of specific genes in R?

I have a list of genes as row-names of my eset like: iDs <- head(rownames(eset)) [1] "LGI1" "ATE1" "NELL1" "CCND1" "FADD" "PPFIA1" "ORAOV1" "FOXN4" "NOVA1" "PTGER2" "GPX2" "DLK1" [13] "ZG16" "MYH2" "NPTX1" How can I find GO…
user3576287
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Variable resetting back to 0 after if statement in python

I am getting this error IndexError: list index out of range and from what I've gathered it is because my r variable is resetting to 0 as soon as it enters the if statement. I'm learning python as I go so any tips and tricks would be greatly…
Georgrio
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How to split a file according to labels using pandas?

I have a genome sequencing file in the following format: chromosome name (string) | location (int) | readings (int) Data for all chromosomes are stored in one single file and I wish to split file into individual chromosome data files; convert…
Machine
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Why are some SNPs assigned to the wrong position or even chromsome

When lifting my genome wide data I came across the issue, that some rs-numbers have merged. That leads me to the point, that a SNP must have been misassigned to the wrong position once (or even to the wrong chromosome). After some time, laboratories…
Mathias
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Which algorithm is good for genetics duplicated data?

My question is more related to find the best algorithm for my data set. I have data which has three columns namely, individuals, and disease and test score (I have 50 test scores features but only one test score feature is mentioned here). I have…
Asif
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R code to work on genotype data

I have this data called mydf. I need to match the letters (DNA letters) in column REF and ALT with the colnames(x) ("A","T","G","C") and get the corresponding numerical values pasted together as "REF,ALT". However, there are some lines where I…
MAPK
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GenABEL: Missing sex "NA" in plant GWAS

I want to use GenABEL for GWAS in a diploid plant species, but GenABEL stuck on as it requires a "sex" column in pheno file. It should be filled with "1" for male or "0" for female. But I am working with a plant species. What should I do? Error in…