Clustering subpopulations using the K-means algorithm
This post will explain how to classify individuals within a population into subpopulations using the K-means algorithm....
Author: poweruser
Clustering subpopulation using deep learning algorithm
This post explains how to predict subpopulation class for individuals given known genomic analytics, using deep learning...
How to create a subset file from SNP dataset
Figure 1 shows the "SNP data filter" tab page selected in QTLmax. The input data is a genome data file (*.ped and *.map)....
How to draw a violin plot with QTL marker data and phenotypic data
Figure 1 shows the "QTL search and haplotype tools" tab page selected within QTLmax. Press the button to open the file...
Fitting a linear mixed-effect model with phenotypic data including environmental factors
Figure 1 shows the "Linear mixed-effect model" tab page selected within QTLmax Workbench. (Figure 1) The input data format...
How to draw a heatmap with phenotypic data
The "Heatmap" tab page has many setting options. If you don't want to select each setting option individually, just click...
How to draw a density plot with phenotypic data
Figure 1 shows the "Density plot" tab page selected within the QTLmax Workbench. (Figure 1)The "Density plot" tab page has...
How to draw a box plot using phenotypic data
shows the QTLmax Workbench with the "Box plot" tab selected. (Figure 1) The Box plot tab has many configuration options....
How to draw a scatter plot matrix
Figure 1 shows QTLmax Workbench with the "Scatter Plot Matrix" tab selected. (Figure 1) The "Scatter Plot Matrix" tab has...
Best linear unbiased prediction
Figure 1 displays the BLUP tab page selected. After clicking the button and selecting a phenotype file in CSV format, the...
Genomic prediction
Figure 1 shows the Genomic Prediction tab page with both genomic and phenotypic data loaded. Once both datasets are input,...
Cross-validation (genomic prediction)
The principle of cross-validation is simple: a population with both genomic and phenotypic data is randomly divided into N...
Visualizing SNP Locations on the Genome by using QTLmax Workbench
In this post, we will perform the task of visually marking specific SNP locations on the genome by using QTLmax Workbench. ...
GWAS procedure (Generalized linear model)
In GLM-GWAS calculations, the imputation step is optional, not mandatory. In this regard, the GLM-GWAS calculation...
Backcross selection
Figure 1 shows the tab page related to backcrossing. The input data for backcross selection is the "similarity_matrix.csv"...
How to create LD heatmaps & Manhattan plots from a defined genomic window
To draw an LD heatmap, you must first set the genomic window range. To see how to set the genomic window, please click the...
How to set genomic window range
Figure 1 shows the "Haplotype tools" tab page selected. The "Haplotype tools" tab page contains tools for haplotype...
How to list QTL Markers
The "QTL search and haplotype tools" tab page supports the extraction of QTL markers using a P-value threshold. Figure 1...
Marker assisted selection (MAS)
Figure 1 shows the MAS (marker-assisted selection) tab page selected. (Figure 1) Copying the SNP list into the 'SNP list'...
How to calculate admixture and plotting admixture bar chart
Figure 1 shows the Admixture tab page selected. On this tab page, you can choose the K values. The K value ensures that the...
How to display SNP data as a table
(Method 1) Figure 1 shows the results of the SNP table for each chromosome. (Figure 1) (Method 2) Figure 2 shows the SNP...
How to perform a genomic control computation
Figure 1 displays the QQ plot generated from the P-values obtained by performing GLM-GWAS calculations with demo data. As...
How to draw a QQ plot
This post will explain how to draw a QQ plot using QTLmax Workbench. When you perform GWAS calculations in QTLmax, the...
How to merge a Manhattan plot
When you perform GWAS calculations in QTLmax, the following result files are generated: genotype.ped genotype.map pvalues...
GWAS procedure (linear mixed model)
Figure 1 shows the LMM-GWAS tab selected. You need to select files a pair of imputed PED and MAP files, a matrix file for...
How to merge a phenotype and a PCA tables
(Figure 1) In the Table 1 and Table 2 boxes, you need to select the column name for sample names and move it to the "ID...
Genetic similarity matrix computation
Figure 1 shows the tab page selected for calculating the "genetic similarity matrix." (Figure 1) Figure 2 shows the result...
PCA computation
Figure 1 shows the PCA tab page selected. (Figure 1) Figure 2 shows the project folder containing the result files after...
Imputation
Figure 1 shows the tab page for the imputation job. For imputation, you need a file in VCF format or VCF.GZ format (a...
GWAS steps (linear mixed model)
1. Imputation (QTLmax ▶ Preprocess ▶ Imputation) 2. PCA computation (QTLmax ▶ Genetic...
How to give new names to all SNPs
Figure 1 shows the SNP naming tab page selected. The SNP naming tab page is a feature that names each SNP. (Figure 1) The...
Brief overview on GUI
A manual installation is required only once when you install QTLmax. From that point on, all upgrade will be occurred...
How to install Linux Mint
QTLmax works on Linux Mint. If you are not familiar with Linux Mint, don't be panic. Linux Mint is user-friendly and offers...