Genetic Variability and Association analysis in R
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- Опубликовано: 7 авг 2024
- Variability is one of the most common research problem for students of Genetics and Plant breeding. The video deals with three aspects of Variability analysis in R
1) Genetic parameters:
Genotypic and Phenotypic Variance, Heritability, Genetic Advance and Genetic Advance as percentage of Mean
2) Genotypic and Phenotypic Correlation
3) Path analysis
Time Stamps:
0:00 Introduction
1:24 Description of dataset and import in R
3:34 Installation of variability package
4:48 Calculation of Genetic parameters like Heritability, GA, GA as % of mean
11:20 Genotypic and Phenotypic correlation
16:21 ANCOVA and calculation of Genotypic & Phenotypic Covariance
17:30 Path Analysis
Link for blog
Part I: Genetic parameters
/ variability-analysis-i...
Part II: Genotypic & Phenotypic correlation
agriculturalstatistic.blogspo...
Part III: Path Analysis
agriculturalstatistic.blogspo...
Dataset link
drive.google.com/file/d/1sda2...
Link for formulas
drive.google.com/file/d/1SCyn...
If you are using the variability R package in research work you can cite it as:
Raj Popat, Rumit Patel and Dinesh Parmar (2020). variability: Genetic Variability Analysis for Plant Breeding Research. R package version 0.1.0.CRAN.R-project.org/package=va...
Suggestions comments and Quires are welcomed
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#genotypicpathanalysis
#geneticparameters
#heritability
#genotypiccorrelation
#geneticsandplantbreeding
#pathanalysis
Genotypic Correlation with interpretation and heat map
ruclips.net/video/FPRTDPXUz90/видео.html
Phenotypic Correlation with interpretation and heat map
ruclips.net/video/kc2Nlp0GuPg/видео.html
Phenotypic Path Analysis with interpretation
ruclips.net/video/3T5dQ77YgoI/видео.html
Genotypic Path Analysis with interpretation
ruclips.net/video/KLTupZUVfic/видео.html
Calculation of Genetic parameters like genetic advance, genetic advance as percentage of mean, heritability etc
ruclips.net/video/s_hRJOf8hww/видео.html
Very easy to use platform
a very informative and good explanation for new R users
Very useful to genetics and plant breeding students. Just write five lines and your MSc research complete. Kudos🙌
Thank you for this kind words🙏
Why we need to drop the trait whose genotypic variance is negative?
Ans:
genotypic correlation (trait1,trait2)=Covariance (trait1,trait2)/ Square root (Variance (trait1)*Variance (trait2))
Since we need to take Square of Genetic Variance if it's value is negative it will generate NaN. So we remove the trait having negative genotypic Variance.
Hope you get the reason!
Regards
RAAJ
Sir thank you so much for introducing a good package for variability analysis.
Very useful package. Thanks for sharing this video.
Welcome 🙏
Thank you very much for providing this important information and also we need on other d/t experimental design
Great work. Many many thanks
Hi.... please keep it up with more such videos.... very nice
Thank you 🙏
Thank you very much for your clear presentation. I did my data analysis based on your presentation. I will cite you name.
Glad it was helpful!
Thanks a lot, good video.
hi.. I want to know that for analysis of augmented design data, what will be a better approach ? Linear mixed effect model using lme4 or the AugmentedRCBD?
very useful sir thank u
Thanks, the video is helpful. How to do it for a partially balanced incomplete block design?
Thanku so much... It helped me a lot
Thank you for the detailed information... Kindly tell how to save all these analysis in xlsx format.... (Excel)
Thank you very much, Sir
It is for RCBD analysis. Can you tell me how i can perform all these variability analyses for CRD also??
also need this analysis video plz Varibility analysis in R - II: Genotypic and Phenotypic correlation
Thank you
Morning sir and thanks for the video. I not able to run the analysis cause it's giving me error in contrast as result. What can I do? Thanks
Check out this path diagram and make necessary changes manually as per your results.
drive.google.com/file/d/1_t6wp6HkgDDYKpT4MEAFlxVTebYQY_O6/view?usp=sharing
Please don't edit the file just download it
Regards
RAAJ
Can you please tell how to make diagram out of path analysis data in R?
Great, thanks very much
You are welcome!
Sir how we will arrange the data for genotypic and phenotypic correlation if we have four different treatments? how we develop combine correlation of four treatments?
Thanks for for your video, could you please tell me how to calculate narrow sense heritability by R?
Thanks more, for your information. would you send me please, the package on variability analysis for partially incomplete block (simple lattice) design?
Great sir
Thank you 🙏
Please make a video on Principal component analysis (PCA) and Heatmap on RStudio
Thanks for suggesting the topic
please quick
Sir, how to analyze F2 data where there is no any replication? Could you please suggest how to do genotypic and phenotypic correlation and path analysis in F2 data?
How can we do Variability analysis for multi environment data conducted using RCBD ? I need help how to write the script
You explained very well.
Please help me in my query, I have 66 genotypes in 2 replication but with the gen.var function i am getting a degree of freedom for genotypes as 64, it should be 65. Why this is so
Thank you soo much at last I found what I am searching for my MSc Research😊
🙏
Is their any packages for triallel and quadriallel analysis
Sir upto which range we can get residual value... What we have to do to reduce the residual value
Sir can u please give me a overview what is population genetic analysis in plant ?????Tommorow is my interview i have to go through this ease
What is commend line for two year RBD ANALYSIS?
Can we analyse the environmental correlation?
Sir, kindly make a video on AMMI analysis in R
Please make a video on AMMI model for stability analysis
Did u take the average of the phenotype for each plot?
sir i follow all step but when i run I error occur like this what i do plz help .
> gen.var(vardata[3:13], vardata$Genotypes, vardata$Replication)
Error in gen.var(vardata[3:13], vardata$Genotypes, vardata$Replication) :
could not find function "gen.var
You might have forgotten to load the Variability package.
Please load the package & than try again.
To load package type
library (variability)
Regards
RAAJ
@@agrianalyze thankx
i have done now want to export it into word or xl file what i do now plz any guide
Sir I am also facing same problem ...I checked variability package was attached to it...but same thing was happening
Can i use same procedure in pooled CRD sir
Thank you for the nice and clear presentation, it is very usefull, however could you please give us how to do path diagram script
There is ppt in description box. You can use that
I checked the ppt, there is a diagram path but i need to have the script, could you give us a clear video presentaion with clear steps in rstudio. Thank you in advance forr the usefull information that you gived to us.
who to do cluster distance?
What is the code to generate the path analysis graph? Could you teach us? Thank you, excellent video.
There is link given in comment box for downloading a path diagram used in MSc thesis. You can download and use it.
Regards
Raj
@@agrianalyze Thank you. I do all the process of video but when i do the phenotypic a genotypic analysis the results are very large numbers, for example: 371.64, think that I have a problem because found several analyzes where the results of this are like yours, numbes in a sale of 0 to 1 positive or negative.
how can we calculate phenotypic path analysis without replication
I want to do variability analysis for alpha lattice design. Will the procedure be different?
This package is confined to Variability analysis using RCBD design only.
Thank you, how we can do if we add years and locations, also AMMI and GGE biplots
Metan package in R!
Thanks for this quite helpful video. One question: are the functions in this package (variability) can only be applied on data with same replications? I.e. if g1 has three replication, g2 has four replication..., functions will make mistakes?
Th analysis is based on randomised block design and in this design the number of replication is fixed. So all the genotypes must have same number of replications.
@@agrianalyze Thanks for the answer. Do you know any packages or function in R which calculate genetic parameters with different replications? Like variance analysis in SAS, data with same replication use ANOVA function while data with different replication use GLM.
Sorry I didn't know about it!
@@agrianalyze Never mind. Thanks a lot for your kind help
Thanks for making a valuable video for plant breeder. I have done a experiment following augmented design. There, check varieties replicated 3 times but genotype was non replicated. Does the variability analysis for this augmented design will be same ? If not, how to do it. Also suggest about the correlation and path of same design
Namaskar Abu
Please refer augmented RCBD package.
Regards
RAJ
@@agrianalyze Thanks for valuable suggestion. But I got only ANOVA and descriptive statistics from AugmentedRCBD packages. I also need variability analysis like phenotypic & genotypic correlation, path analysis from augmented design. Please give a suggestion. Better, you upload a video above the analysis of augmented design using R studio. Advanced thanks for upcoming video.
I'm using same instruction for 22 variables including genotypes and replication but when I start to command then
Error: unexpected '{' in "geno.corr(file name {"
I don't know brother
what is mean by NaNs in geno corr analysis
As genotypic variance is negative so correlation cannot be found.
Please read the note given after correlation matrix.
I have used 16 traits, but results are comming only for 8 traits. But, the 6 traits are having not available (NA) data.
Does the variability analysis for augmented design will be same ? If not, how to do it. Also suggest about the correlation and path of same design
The analysis is different. For that you need to use augmentedRCBD package in R. It has all the necessary function.
go for augmentedRCBD package
@@vaibhavchittora1579 But augmentedRCBD doesn't provides the option to estimate genetic variability parameters right?
Sir 3 replication k liye bhi same proces hoga ky data arrangement continue rhega ky
IN R STUDIO WHICH PACKAGE IS SUITABLE FOR GENERATION MEAN ANALYSIS
I am not sure but please check R package named "plantbreeding"
Please bring PCA and regression analysis in R
Thanks for suggesting topic
sir please reply..1.) how to do d^2 analysis? ....2) i did path with O.P stat it is showing residual data 0.0648....while r studio showing 0.0062..for same data..all gm are matching all correlation are matching...but not path....3.) sir what about independent variable(seed yield per plant) it hsould be in last coloum ....in OP stat there is cololum for independent variable but not in R studio.....4.) how can i get diagrams of path and cluster analysis....please reply......
1) I don't know about analysis of D 2 in R
2) While developing this package it was cross checked with SPAR output so output from variability package seems promising to me for residual values in path analysis
3) In this video at 1:34 on wards discussion about data arrangement in excel is discussed. You should place dependent variable in last column or first column but not between independent variables.
4) I am sharing a link for path analysis diagram. You need to edit diagram as per your results.
Regards
RAAJ
drive.google.com/file/d/1_t6wp6HkgDDYKpT4MEAFlxVTebYQY_O6/view?usp=sharing
@@agrianalyze i m very very thankful to you...🙏
D square analysis using Indostat
Sir how to do variability in F2 generation because it will not be having replicated data
Sorry I don't have idea about it
Wat is the codes for path analysis in augmented design
medium.com/@popatrajc/variability-analysis-in-r-i-genetic-parameters-26f9ee90e741
Sir Thanks very much for this information but path diagram make pleas edit
Which R Studio version is this ?....I can't import data
If you are using for the first time make sure that device is connected to internet so that it can automatically download package necessary for importing excel file
sir will this script work for alpha lattice design?
This function are made for RCBD
Excellent...sir , but how to save to an fiile.
Thank you 🙏
Directly copy paste the output from console to Word or Notepad.
You can also use sink() function to save the output
@@agrianalyzeThank you sir
Error in `contrasts
Facing the same problem
how can we draw path diagram in R
Check the link of the pinned comment in this video
How do we export the results in console to excel?
use write.xlsx() function of xlsx package
@@agrianalyze Worked!
Thanks
@@hamzaashfaq4869 sir how to exporte result detail commond share me sir
@@BAJRANGKUSRO i used sink command to export.
First create a dataset.. like
dataset
Error in lapply(X = X, FUN = FUN, ...) : object 'varadata' not found please share the answer for my error
Hi you need to rename your data fiel as vardata while importing
How to this this analysis in excel sir also genetic divergence analysis in CRD design
Do analysis as per RCBD and later merge replication component with error
@@agrianalyze thank you sir also how to do d square analysis
hI, I HAVE SINGLE REPLICATION DATA, THIS CODE IS NOT WORKING FOR VARIABILITY
The script is for genotypes for rbd design. Your data seems to be of augmented design. Consider Augmented RCBD package
Genotypes are hybrids or lines?
In this example, genotype are Lines. The data is pertaining to different 28 lines.
Excellent package. Thank you. I have sent an email to you. Please respond.
Thanks for the appreciation. Had not received your email. You can email me at popatrajc@gmail.com
function gen.var is not available how to install
Install and load variability package
@@agrianalyze how to find cd value in analysis report of alpha lattice design in which cd value not came
Sir how to install r studio
First install R in your system followed by Rstudio.
cran.r-project.org/bin/windows/base/
www.rstudio.com/products/rstudio/download/
Sir r studio download but package are not working
Thankyou so much sir given information 😊😊
Sir how to result exported to excel file par video banaiye sir
For sure ! Thank you for your suggestion. You can export using write.xlsx() from xlsx package.
You need to check the formula for heritability in the package. Heritability doesn't come out right.
Thank you for the suggestions. I will look into it!
Regards
Raj
@@agrianalyze the error term component that makes up the phenotypic variance should be devided by the number of replications.
reply me soon plz
For d2 analysis contact me.