GEBV Calculators

Owned by Star Yanxin Gao
May 12, 2020
5 min read


Created by Star Yanxin Gao, last modified on Aug 31, 2018

The default phenotype file to run GEBV calculator: 

  1. samples stored in rows

  1. contain the same set and number of samples as in the genotype file, already pre-sorted in the exact same order, see 

3. Sample Matching tool; samples genotyped but not phenotyped

  1. phenotypic data need to be numeric values,

  1. one or multiple columns of phenotypic observations are allowed

  1. Only one header row on the top in the file

Here is an example of phenotype input file

The default marker matrix genotye file to run GEBV calculator:

  1. samples stored in rows in the same orientation as in the phenotype file-use transpose function within GEBV tool when the input marker matrix genotype file contain markers in rows and samples in columns 

  1. the same set and number of samples as in the phenotype file, already pre-sorted in the exact same order, see 

3. Sample Matching tool

  1. marker data need to be numeric values, see Encoding tool 

Encoding to convert non-numeric marker matrix data to numeric data

  1. only one header row on the top in the top

  1. the first marker data point start in the 2nd row and first column, i.e. sample header removed from the first column

Here is an example of genotype input file Genotype-markers in column.txt in the same orientation as the phenotype file



  1. Click on the “

Get Data” menu link placed at the left side:

  1. Click on the “

Upload File from your computer” tool link:



 

 

  1. Push the “Choose local file” button:

  1. You can choose two (typical) or more data files to upload. Push the “Start” button. The “Status” column will show how the upload(s) are progressing. If they finish by any file type as ”.csv”, for example, it is automatically detected after its upload being done. We are using two files: Test_Grain_PhenotypeforrAmpSeq.csv and GenotypesForGS.csv



  1. Once such two csv data files being successfully uploaded and identified, click on the “Close” button:



  1. The new data are shown at the right side and they are disposed to be used by BGLR. Now click on the “

GOBII Tools” menu link placed at the left side:

 

  1. Click on the “

Bayesian Generalized Linear Regression calculator” tool link:

  1. You can see the input values of the “

Bayesian Generalized Linear Regression calculator” (BGLR) tool:

  1. Choose one of the two csv data files, Test_Grain_PhenotypeforrAmpSeq.csv, for the first file input value, “Input Phenotype File”:

 

10)   The following five input values are already filled with their values by default, verify them:

11)   Roll the screen down until getting the “Incidence Matrix and Model” as the first row and push its button associated, “+ Insert Incidence Matrix and Model”:

12)   Choose the second and last csv data file, GenotypesForGS.csv, for the second file input value, “GenotypesForGS” and Fixed for the “Model” input value:



13)   The following four input values are already filled with their values by default, verify them:

14)   Roll the screen down until getting the “SaveAt” input value as the first row and verify all the six input values shown that they are filled with their values by default:



 

15)   Roll the screen down until getting the “Groups Vector Colum” input value as the first row and verify that the last two input fields are filled with their values by default:



Note that we are using no cross validation now. There are the other cross validations available: “K-Fold Cross Validation” and “Leave-p-out (LPO)”. Each one of these two ones have its own input values by default. Also, there is online documentation below describing each one of all the input values:

16)   We are done with entering all the input values! Now push the “Execute” button:

17)   There should be three rolling icons appearing in the right side. Give them about a half minute and three new output data (generated) should appear in the right side:

18)   Click on the “Eye” icon of the first link placed on the right side and the output data is numerically shown in the CSV format:

19)   Click on the “Eye” icon of the second link placed on the right side and the output data is graphically shown in the PDF format:

20)   Click on the “Eye” icon of the third link placed on the right side and the output data is graphically shown in the PNG format:

Download output results

  1. Click on the “

Bayesian Generalized Linear Regression on data 1 and data 2” output data link placed at the left side:



  1. Click on the diskette icon to begin the download of the BGLR output data in the CSV format:



  1. Once the download being done, the BGLR output data is available in your Downloads folder depending on the Internet browser you are using:



  1. Repeat the steps 1) and 2) to download the same BGLR output data but in the PDF or PNG format in the Downloads folder: