genetics

Gene ontology (GO) analysis for a list of Genes (with ENTREZID) in R?

由 纵饮孤独 提交于 2019-12-12 17:05:00
问题 I am very new with the GO analysis and I am a bit confuse how to do it my list of genes. I have a list of genes (n=10): gene_list SYMBOL ENTREZID GENENAME 1 AFAP1 60312 actin filament associated protein 1 2 ANAPC11 51529 anaphase promoting complex subunit 11 3 ANAPC5 51433 anaphase promoting complex subunit 5 4 ATL2 64225 atlastin GTPase 2 5 AURKA 6790 aurora kinase A 6 CCNB2 9133 cyclin B2 7 CCND2 894 cyclin D2 8 CDCA2 157313 cell division cycle associated 2 9 CDCA7 83879 cell division cycle

Generating Random Variables with given correlations between pairs of them:

由 天涯浪子 提交于 2019-12-12 08:54:45
问题 I want to generate 2 continuous random variables Q1 , Q2 (quantitative traits, each are normal) and 2 binary random variables Z1 , Z2 (binary traits) with given pairwise correlations between all possible pairs of them. Say (Q1,Q2):0.23 (Q1,Z1):0.55 (Q1,Z2):0.45 (Q2,Z1):0.4 (Q2,Z2):0.5 (Z1,Z2):0.47 Please help me generate such data in R. 回答1: This is crude but might get you started in the right direction. library(copula) options(digits=3) probs <- c(0.5,0.5) corrs <- c(0.23,0.55,0.45,0.4,0.5,0

Max Fitness stuck at local maxima in genetic algorithm implementation

由 限于喜欢 提交于 2019-12-12 03:39:46
问题 Having trouble with this code below. It is implementation of population evolution. In my case the max fitness is struck at a local maxima everytime and is unable to reach max possible value. Kindly suggest necessary edits and reason for the same. Individual.java package genetic.algorithm.project; import java.util.Random; public class Individual { public static int SIZE = 300; private int[] genes = new int[SIZE]; private double fitnessValue = 0.0; // Getters and Setters public void setGene(int

Minor allele frequency matching?

由 余生长醉 提交于 2019-12-12 01:37:00
问题 I have a list of SNPs that I have already obtained their proxy SNPs with MAF and LD from 1000 genomes pilot 1. I want to know when everybody mentions about MAF matching, do they need to be exactly the same? For example, the SNP of interest has MAF 0.35, if the proxy SNP has MAF 0.37, can it be used as a good proxy? Given LD of the two >0.8 Do have absolutely have to choose a proxy that has a MAF equals 0.35? 回答1: LD as measured by R-sq is dependent on MAF ie high R-squared implies MAFs are

High-level data matching between 2 tables

由 岁酱吖の 提交于 2019-12-11 19:23:02
问题 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 ENSG00000064419 7.7461 rs12537284 ENSG00000064419 4.5544 rs3764650 ENSG00000064666 12.3401 rs10479002 ENSG00000072682 5.0141 rs6704644 ENSG00000072682 6.2306 rs2900211 ENSG00000072682 9.9022 Table 2: Best_SNP Gene Best_Pval rs9028922 ENSG00000007341 10.7892 rs8233293 ENSG00000064666 89.342

Neo4j cypher query for X-chromosome ancestors

由 时光毁灭记忆、已成空白 提交于 2019-12-11 02:32:14
问题 In genetic genealogy X-chromosome data is useful linking to certain ancestors. This is well illustrated at: X-DNA Inheritance Chart My Neo4j database has nodes for each Person and relationships connecting them of father and mother. Each node has a property sex (for the Person's gender; M or F). A female has two X-chromosomes, one from either parent. A male has one X-chromosome, always from the mother. You can use reduce to see the genders involved in the inheritance from ancestors: match p=(n

Converting nucleotides to amino acids using JavaScript

由 最后都变了- 提交于 2019-12-10 09:25:15
问题 I'm creating a Chrome Extension that converts a string of nucleotides of length nlen into the corresponding amino acids. I've done something similar to this before in Python but as I'm still very new to JavaScript I'm struggling to translate that same logic from Python to JavaScript. The code I have so far is the below: function translateInput(n_seq) { // code to translate goes here // length of input nucleotide sequence var nlen = n_seq.length // declare initially empty amino acids string

How to map a list of SNPs to genes?

由 。_饼干妹妹 提交于 2019-12-08 11:31:24
问题 I have been searching the answer to this question for a while. It seemed like it would not be hard to solve at first, but it seems quite challenging now. I am searching for a way to submit a list of of SNPs (rs#) and get back a list of the genes these markers map to. So far I have mostly ways to map SNPs to diseases, pathways, etc. Or to use genes to get a list of representative SNPs. Also, I am quite new to computational biology, so I would appreciate a solution that doesn't rely heavily on

Converting nucleotides to amino acids using JavaScript

由 旧巷老猫 提交于 2019-12-05 18:01:48
I'm creating a Chrome Extension that converts a string of nucleotides of length nlen into the corresponding amino acids. I've done something similar to this before in Python but as I'm still very new to JavaScript I'm struggling to translate that same logic from Python to JavaScript. The code I have so far is the below: function translateInput(n_seq) { // code to translate goes here // length of input nucleotide sequence var nlen = n_seq.length // declare initially empty amino acids string var aa_seq = "" // iterate over each chunk of three characters/nucleotides // to match it with the

How to plot positions along a chromosome graphic

由 血红的双手。 提交于 2019-12-04 09:28:52
问题 I would like to generate a plot depicting 14 linear chromosomes for the organism I work on, to scale, with coloured bars at specified locations along each chromosome. Ideally I'd like to use R as this is the only programming language I have experience with. I have explored various ways of doing this e.g. with GenomeGraphs but I have found this is all more complicated than what I want/ displays a lot more data than what I have (e.g. displaying cytogenic bands) and is often specific for human
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