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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Why does R coerce "0" as character to NA when converting to numeric?

I am analyzing a genetic sequence in R. The columns of the dataframe are the SNPs, and the rows are individuals. The genotype for each individual in the sample for that SNP is recorded as a character, like "CC", "AC", "AA". Since there are only…
KVemuri
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Using awk in if statements

I have a data file that looks like this: 1 . 0 10109 AA AA 1 . 0 10123 C CCCT 1 . 0 10133 A AAC 1 . 0 10134 A ACAAC 1 . 0 10140 A ACCCTAAC 1 . 0 10143 C CTACT 1 rs144773400 0 10144 T …
mfk534
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Reverse complementary Base

I'm new to R programming and I'm trying to write a program for Reverse and Complementary Base. The objective is to design a DNA primer. So I have a DNA sequence with bases A T C G and A complement to T; T=A;C=G;G=C. I figured out how to reverse it…
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Total Mismatches between two strings

I am looking for a way to find the total number of mismatches between two strings in python. My input is a list that looks like this ['sequence=AGATGG', 'sequence=AGCTAG', 'sequence=TGCTAG', 'sequence=AGGTAG', 'sequence=AGCTAG',…
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Building .sif file from microarray ,tab file with expression valuses and gene id only

How to generate a .sif (simple interaction) file from gene micro array expression .tab file containing only gene expression values and gene names? I use Expander software and MeV and want to build an input file for Cytoscape and Spike software. Is…
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Redirecting vcftools file in linux - tips

Here is the code that gets the VCF file from a specific region using tabix and then filters it for specific (european) population using 'keep' option from vcftools. ####select specific population if [ "$POP_FILE" != "" ]; then vcftools --vcf…
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Create VCF from .bim, .bed and .fam files

I have a .fam, .bed and .bim file with markers for few individuals. I would need to convert it into a VCF file. Could someone help to create a VCF file. Are there any opensource tools which can do this?
chas
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Z-scores rounded to infinity for small p-values in R

I am working with a genome-wide association study dataset, with p-values ranging from 1E-30 to 1. I have an R data frame "data" which includes a variable "p" for the p-values. I need to perform genomic correction of the p-values, which I am doing…
user3745089
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Python numpy efficiently combining arrays

My question might sound biology heavy, but I am confident anyone could answer this without any knowledge of biology and I could really use some help. Suppose you have a function, create_offspring(mutations, genome1, genome2), that takes a list of…
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Somehow not assigning a class with Ruby

On runtime, my code often come into an undefined method error for the method mate. As far as I can figure, a Person somehow slips through the cracks sometime along the code's exucution, and manages not to have an allele assigned to it. Code…
deeb
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Graphing Genotypes w/ R plot or hist

I am doing a very simple simulation using hardy-weinberg (for all you genetics junkies) and I am having a terrible time plotting out the frequencies of allele (0,1) frequencies and finally genotypes (0,1,2) frequencies over the course of a 100…
mccurcio
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Create dictionary, only adding rows where one column matches a value in a list

I've got 2 CSV files. First, I want to take 1 column and make a list. Then I'd like to create a dictionary from another CSV, but only with rows where the value from one column matches a value already in the list created earlier on. Here's the code…
cps1
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Matching and merging two text tables?

I have 2 (pretty big, ~15k lines) csv tables in the following formats: Disease/Trait Mapped_gene p-Value Wegener's granulomatosis HLA-DPB1 2.00E-50 Wegener's granulomatosis TENM3 - DCTD 2.00E-06 Brugada…
cps1
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Implementing the Viterbi algorithm in a HMM with changing emission matrices across genomics markers

I would like to ask for help in implementing a hidden markov approach to assigning ancestry based on SNP genotype data. Given that I have a transition matrix generated as such: states <- c("A1","A2","A3","A4","A5","A6","A7","A8") # Define the names…
user2895292
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Looping regressions

I have a dataset of 2000 gene expression variables with 62 observations and want to obtain the p-value from regressing each of the variables on a class variable (which is either 1 meaning healthy or 2 meaning has a tumour) and want to regress each…
user2958701
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