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.

312 questions
0
votes
1 answer

Apply function to every 20 rows between pairs of columns in a matrix

I have a set of genetic SNP data that looks like: Founder1 Founder2 Founder3 Founder4 Founder5 Founder6 Founder7 Founder8 Sample1 Sample2 Sample3 Sample... A A A T T T T T A T A T A A A T T T T T A T A T A A A T T T T T A T A T A A A T T T T T A T A…
user2895292
  • 63
  • 1
  • 6
0
votes
1 answer

R Programing, Read in and Run multiple files

I'm using a program called COLONY from some genetic analysis. Colony has an R package (rcolony). What I need to do is move text files from a directory ("C:/GenSoftware/Colony/datFiles") into another directory ("C:/GenSoftware/Colony/") rename it…
John Anderson
  • 67
  • 1
  • 6
0
votes
1 answer

High-level data matching between 2 tables

I'm new to R and I need advice on dealing with this problem: I have 2 tables. The start of the tables are shown below: Table 1: SNP Gene Pval Best_SNP Best_Pval rs2932538 ENSG00000007341 5.6007 rs10488631 …
zfz
  • 153
  • 3
  • 16
0
votes
2 answers

How to compare two tables based on a changing specification

I have two tables, the start of each is given below: Table 1: All SNPs SNp Gene rs1798922 ENSG00000167634 rs4677723 ENSG00000167634 rs1609823 ENSG00000104450 rs11597390 ENSG00000104643 rs7824557 ENSG00000104643 rs1371867 …
zfz
  • 153
  • 3
  • 16
0
votes
1 answer

How to use DWD R package in order to remove biases and merge two microarray datasets

I am trying to find a way to use distance weighted discrimination method (DWD) to remove biases from multiple microarray datasets. My starting point is this. The problem is that Matlab version runs only under Windows, needs excel 5 format as input…
gc5
  • 9,468
  • 24
  • 90
  • 151
0
votes
1 answer

why Hardy-Weinberg test is different in GenABEL and Plink?

When I use this Plink command: Plink --file filename --hardy will create a new file filename.hwe with the different p-value for each marker, by contrast with GenABEL…
Hocine Ben
  • 2,079
  • 2
  • 14
  • 20
0
votes
1 answer

simulation of genetic data in R

I am looking for the best way or best package available for simulating a genetic association between a specific SNP and a quantitative phenotype, with the simulated data being the most similar to my real data, except that I know the causal variant.…
-1
votes
0 answers

How do I use PLINK to calculate the genetic distance cM between two samples?

I have download PLINK from https://www.cog-genomics.org/plink/, I have download a genetic map from…
Anon21
  • 2,961
  • 6
  • 37
  • 46
-1
votes
1 answer

Using glm in R for linear regression on a large dataframe - issues with column subsetting

I am trying to use glm in R using a dataframe containing ~ 1000 columns, where I want to select a specific independent variable and run as a loop for each of the 1000 columns representing the dependent variables. As a test, the glm equation works…
-1
votes
4 answers

Adjusting the fucntion to find location for more than one base

I created this function and it finds the location of the base in a dna sequences. Like dna = ['A', 'G', 'C', 'G', 'T', 'A', 'G', 'T', 'C', 'G', 'A', 'T', 'C', 'A', 'A', 'T', 'T', 'A', 'T', 'A', 'C', 'G', 'A', 'T', 'C', 'G', 'G', 'G', 'T', 'A', 'T'].…
-1
votes
1 answer

How to run PLINK on m1 MacBook

I am a new user of PLINK. I installed plink1.07 on the website and followed the instruction. However, my terminal returned no file when I type ./plink. Here is the return: zsh: no such file or directory: ./plink
Chris
  • 95
  • 5
-1
votes
2 answers

Python Regex Finding a Match That Starts Inside Previous match

I'm looking to find the index for all substrings in a string in python. My current regex code can't find a match that has it's start in a previous match. I have a string: s = r'GATATATGCATATACTT' and a subtring t = r'ATAT'. There should be matches…
Oliver
  • 281
  • 3
  • 14
-1
votes
1 answer

lookup for values in two columns in the presence of duplicates in R (edited)

As a newbie I'm struggling to solve the following issue with a big dataset. I would want to look for the value in the "CHROM" column comparing two columns of CLONEID (the second column contains duplicates). The corresponding "CHROM" value would be…
Marilou
  • 31
  • 8
-1
votes
1 answer

How to remove leading zero from chromosome:position numbers?

I'm trying to extract information from two genetic files based on chromosome position which are in the format 01:23456 and 1:23456. Can you please help me with a code to either remove zeros from the first file (only from 01 to 09, because the rest…
Doodle
  • 11
  • 6
-1
votes
1 answer

Find a location of a virus gene on a virus-integrated human gene by frequency

I have a virus gene-integrated human gene in data frame or text file form like: "C""G""C""T""G""T""T""G""T""T"... It is 50000 nucleotides long. I have also the virus gene data frame and I found its standard deviation and mean frequency before. I'm…
Amy
  • 11
1 2 3
20
21