Definitions of Phenotype and Genotype - Stack Overflow
May 2, 2015 · Can someone help me understand the definitions of phenotype and genotype in relation to evolutionary algorithms? Am I right in thinking that the genotype is a representation …
r - PCA Biplot variable label customization - Stack Overflow
Sep 26, 2023 · I am trying to make PCA biplot by using follwoing code from the given data. In the data there are 4 type of genotypes, belongs to 4 type of species and 4 types of variables were …
How to recode missing genotype code is - Stack Overflow
Jun 29, 2021 · I'm trying to impute genotype data from the public reference panels but my files fail the file sanity check on Sanger Imputation server and it gives the following error: failed sanity …
In vcf file, retain only variants fulfilling certain QC criteria
Jan 5, 2025 · I have a vcf file containing variants merged from 500 individuals. However, there was minimal filtering done prior to merging. I want to eliminate SNVs in a sample if it does not …
Coding genotypes from nucleotides to 0/1/2 in R (or Python)
Jun 16, 2015 · Most people here don't work with biology and don't know what genotype coding is. Can you briefly explain that and/or show your expected result?
r - Nesting a random factor in GLM (M) - Stack Overflow
Nov 28, 2023 · I want to run a GLMM in R with a random effect that is nested into one of my fixed effects. To describe the data a little bit: genotype has 24 levels, and I would like to nest this …
calculate per site and sample missingness using tetraploid …
Apr 16, 2024 · I have a vcf file with tetraploid genotype calls, and would like to filter snps and samples based on the proportion of missing genotype calls for each snp and sample. I haven't …
ggplot2 manually specifying colour with geom_line - Stack Overflow
Oct 5, 2014 · 13 I'm trying to plot the graph below, and want to manually specify colours. I need to plot by genotype, since there are multiple genotypes belonging to the same Bgrnd_All, and I …
How to create a MAP/PED file from a dosage file on PLINK 2.0
Nov 10, 2020 · I am new to PLINK and GWAS studies. I am unsure how to write a script to convert my INFO file or dosage data into a MAP file for an association study between …
How to make a normal distribution graph from data frame in …
Feb 27, 2022 · my question is how to make a normal distribution graph from data frame in Python. I can find many information to make such a graph from random numbers, but I don't know how …