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Genetic Variability and Association analysis in R

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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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Carefree by Kevin MacLeod incompetech.com
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Free Download / Stream: bit.ly/_carefree
Music promoted by Audio Library • Carefree - Kevin MacLe...
#genotypicpathanalysis
#geneticparameters
#heritability
#genotypiccorrelation
#geneticsandplantbreeding
#pathanalysis

Опубликовано:

6 авг 2024

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Комментарии : 140

@agrianalyze 4 месяца назад

Genotypic Correlation with interpretation and heat map ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-FPRTDPXUz90.html Phenotypic Correlation with interpretation and heat map ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-kc2Nlp0GuPg.html Phenotypic Path Analysis with interpretation ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-3T5dQ77YgoI.html Genotypic Path Analysis with interpretation ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-KLTupZUVfic.html Calculation of Genetic parameters like genetic advance, genetic advance as percentage of mean, heritability etc ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-s_hRJOf8hww.html

@radhichhag4372 4 месяца назад

Very easy to use platform

@josephchavda4589 3 года назад

Very useful to genetics and plant breeding students. Just write five lines and your MSc research complete. Kudos🙌

@agrianalyze 3 года назад

Thank you for this kind words🙏

@agrianalyze 3 года назад

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

@vaibhavchittora1579 3 года назад

a very informative and good explanation for new R users

@md.shahriarkobir5191 2 года назад

Great work. Many many thanks

@prasadvadigeri4039 3 года назад

Sir thank you so much for introducing a good package for variability analysis.

@damotanteneh4360 2 года назад

Thank you very much for providing this important information and also we need on other d/t experimental design

@Rutvi_patel_1111 3 года назад

Very useful package. Thanks for sharing this video.

@agrianalyze 3 года назад

Welcome 🙏

@SimranjitKaur-gb2vd 3 года назад

Hi.... please keep it up with more such videos.... very nice

@agrianalyze 3 года назад

Thank you 🙏

@md.mukulmia4374 Год назад

Thanks a lot, good video.

@fikirteassefa7939 7 месяцев назад

Thank you very much for your clear presentation. I did my data analysis based on your presentation. I will cite you name.

@agrianalyze 6 месяцев назад

Glad it was helpful!

@jyothsna_jb 2 года назад

Thank you very much, Sir

@monisham4277 Год назад

very useful sir thank u

@poopingboy9637 3 года назад

Great, thanks very much

@agrianalyze 3 года назад

You are welcome!

@shikhadubey2251 2 года назад

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?

@nirija4158 2 года назад

Thanku so much... It helped me a lot

@basazinewdegu4181 2 года назад

Thanks, the video is helpful. How to do it for a partially balanced incomplete block design?

@agriconceptlearning4153 2 года назад

Thank you for the detailed information... Kindly tell how to save all these analysis in xlsx format.... (Excel)

@rumitpatel6622 3 года назад

Great sir

@agrianalyze 3 года назад

Thank you 🙏

@asmashaheen5372 3 года назад

Please make a video on Principal component analysis (PCA) and Heatmap on RStudio

@agrianalyze 3 года назад

Thanks for suggesting the topic

@RAVI-talks 3 года назад

please quick

@truongphu7407 Год назад

Thanks for for your video, could you please tell me how to calculate narrow sense heritability by R?

@faozyathaminou7699 3 года назад

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

@botanyresearchsolutions4849 3 года назад

also need this analysis video plz Varibility analysis in R - II: Genotypic and Phenotypic correlation

@asmashaheen5372 3 года назад

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?

@bhumikasinghlodhi6632 Год назад

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

@tayoolatunji7079 13 дней назад

Thank you

@muhammaduzair3659 3 года назад

It is for RCBD analysis. Can you tell me how i can perform all these variability analyses for CRD also??

@yaziegenet6551 2 года назад

How can we do Variability analysis for multi environment data conducted using RCBD ? I need help how to write the script

@seenaamulatu3825 2 года назад

Thanks more, for your information. would you send me please, the package on variability analysis for partially incomplete block (simple lattice) design?

@niveditashettigar452 3 года назад

Can you please tell how to make diagram out of path analysis data in R?

@darshanraj1939 Год назад

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?

@asmashaheen5372 3 года назад

Thank you soo much at last I found what I am searching for my MSc Research😊

@agrianalyze 3 года назад

🙏

@hiteshkumarsaini1529 2 года назад

What is commend line for two year RBD ANALYSIS?

@prashanthyelimineti2468 2 года назад

Is their any packages for triallel and quadriallel analysis

@sanayakashyap6256 2 года назад

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

@user-gx1ct6hx9n Год назад

Sir upto which range we can get residual value... What we have to do to reduce the residual value

@SHUBHAMSINGH-gh6ln 10 месяцев назад

Did u take the average of the phenotype for each plot?

@shabbirakhtar3662 2 года назад

who to do cluster distance?

@shuyiyang3628 3 года назад

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?

@agrianalyze 3 года назад

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.

@shuyiyang3628 3 года назад

@@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.

@agrianalyze 3 года назад

Sorry I didn't know about it!

@shuyiyang3628 3 года назад

@@agrianalyze Never mind. Thanks a lot for your kind help

@md.abusyed5635 2 года назад

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

@agrianalyze 2 года назад

Namaskar Abu Please refer augmented RCBD package. Regards RAJ

@md.abusyed5635 2 года назад

@@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.

@tonmoychakrabarty2610 3 года назад

Can we analyse the environmental correlation?

@s.husain6125 2 года назад

Can i use same procedure in pooled CRD sir

@cyrinerobbana1691 5 месяцев назад

Thank you for the nice and clear presentation, it is very usefull, however could you please give us how to do path diagram script

@agrianalyze 5 месяцев назад

There is ppt in description box. You can use that

@cyrinerobbana1691 5 месяцев назад

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.

@mayuribarai7624 2 года назад

Please make a video on AMMI model for stability analysis

@uttejkarla8749 3 года назад

Sir, kindly make a video on AMMI analysis in R

@botanyresearchsolutions4849 3 года назад

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

@agrianalyze 3 года назад

You might have forgotten to load the Variability package. Please load the package & than try again. To load package type library (variability) Regards RAAJ

@botanyresearchsolutions4849 3 года назад

@@agrianalyze thankx i have done now want to export it into word or xl file what i do now plz any guide

@vaishnavikhode9178 3 года назад

Sir I am also facing same problem ...I checked variability package was attached to it...but same thing was happening

@getatube16 2 года назад

Thank you, how we can do if we add years and locations, also AMMI and GGE biplots

@gazalaparveen3665 Год назад

Metan package in R!

@diversityboys9602 2 года назад

how can we calculate phenotypic path analysis without replication

@Hxrold1493 2 года назад

What is the code to generate the path analysis graph? Could you teach us? Thank you, excellent video.

@agrianalyze 2 года назад

There is link given in comment box for downloading a path diagram used in MSc thesis. You can download and use it. Regards Raj

@Hxrold1493 2 года назад

@@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.

@vijayrajamanickam6847 Год назад

I have used 16 traits, but results are comming only for 8 traits. But, the 6 traits are having not available (NA) data.

@BAJRANGKUSRO 3 года назад

Sir 3 replication k liye bhi same proces hoga ky data arrangement continue rhega ky

@tonmoychakrabarty2610 3 года назад

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 {"

@agrianalyze 3 года назад

I don't know brother

@shikhadubey2251 3 года назад

I want to do variability analysis for alpha lattice design. Will the procedure be different?

@agrianalyze 3 года назад

This package is confined to Variability analysis using RCBD design only.

@sachinbarad4331 3 года назад

Which R Studio version is this ?....I can't import data

@agrianalyze 3 года назад

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

@deepakkaushik6821 3 года назад

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

@agrianalyze 3 года назад

The analysis is different. For that you need to use augmentedRCBD package in R. It has all the necessary function.

@vaibhavchittora1579 3 года назад

go for augmentedRCBD package

@gazalaparveen3665 Год назад

@@vaibhavchittora1579 But augmentedRCBD doesn't provides the option to estimate genetic variability parameters right?

@prasanthchigurupatii 3 года назад

Excellent...sir , but how to save to an fiile.

@agrianalyze 3 года назад

Thank you 🙏 Directly copy paste the output from console to Word or Notepad. You can also use sink() function to save the output

@prasanthchigurupatii 3 года назад

@@agrianalyzeThank you sir

@botanyresearchsolutions4849 3 года назад

what is mean by NaNs in geno corr analysis

@agrianalyze 3 года назад

As genotypic variance is negative so correlation cannot be found. Please read the note given after correlation matrix.

@sreenivasshrihaan1318 3 года назад

IN R STUDIO WHICH PACKAGE IS SUITABLE FOR GENERATION MEAN ANALYSIS

@agrianalyze 3 года назад

I am not sure but please check R package named "plantbreeding"

@yellankinaveen2496 2 года назад

Error in `contrasts

@bhumikasinghlodhi6632 Год назад

Facing the same problem

@SimranjitKaur-gb2vd 3 года назад

Please bring PCA and regression analysis in R

@agrianalyze 3 года назад

Thanks for suggesting topic

@gopikrishangaur1867 3 года назад

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......

@agrianalyze 3 года назад

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

@gopikrishangaur1867 3 года назад

@@agrianalyze i m very very thankful to you...🙏

@Rin_Chawngthu 2 года назад

D square analysis using Indostat

@shilpan.murthy2174 Год назад

Wat is the codes for path analysis in augmented design

@agrianalyze Год назад

medium.com/@popatrajc/variability-analysis-in-r-i-genetic-parameters-26f9ee90e741

@rtoolsforagriculturer-tag7675 2 года назад

hI, I HAVE SINGLE REPLICATION DATA, THIS CODE IS NOT WORKING FOR VARIABILITY

@agrianalyze 2 года назад

The script is for genotypes for rbd design. Your data seems to be of augmented design. Consider Augmented RCBD package

@Eshwar-zp6qf 2 года назад

Sir how to do variability in F2 generation because it will not be having replicated data

@agrianalyze 2 года назад

Sorry I don't have idea about it

@purnadhanuk5713 3 года назад

sir will this script work for alpha lattice design?

@agrianalyze 3 года назад

This function are made for RCBD

@tarunreddybezawada6678 3 года назад

how can we draw path diagram in R

@agrianalyze 3 года назад

Check the link of the pinned comment in this video

@ranjeetwankhade6772 2 года назад

Sir Thanks very much for this information but path diagram make pleas edit

@yellankinaveen2496 2 года назад

Error in lapply(X = X, FUN = FUN, ...) : object 'varadata' not found please share the answer for my error

@agrianalyze 2 года назад

Hi you need to rename your data fiel as vardata while importing

@hamzaashfaq4869 3 года назад

How do we export the results in console to excel?

@agrianalyze 3 года назад

use write.xlsx() function of xlsx package

@hamzaashfaq4869 3 года назад

@@agrianalyze Worked! Thanks

@BAJRANGKUSRO 3 года назад

@@hamzaashfaq4869 sir how to exporte result detail commond share me sir

@hamzaashfaq4869 3 года назад

@@BAJRANGKUSRO i used sink command to export. First create a dataset.. like dataset

@ulixx63 3 года назад

Genotypes are hybrids or lines?

@agrianalyze 3 года назад

In this example, genotype are Lines. The data is pertaining to different 28 lines.

@sushantgadge7580 Год назад

function gen.var is not available how to install

@agrianalyze Год назад

Install and load variability package

@sushantgadge7580 Год назад

@@agrianalyze how to find cd value in analysis report of alpha lattice design in which cd value not came

@evdivakarasastry 3 года назад

Excellent package. Thank you. I have sent an email to you. Please respond.

@agrianalyze 3 года назад

Thanks for the appreciation. Had not received your email. You can email me at popatrajc@gmail.com

@s.husain6125 2 года назад

How to this this analysis in excel sir also genetic divergence analysis in CRD design

@agrianalyze 2 года назад

Do analysis as per RCBD and later merge replication component with error

@s.husain6125 2 года назад

@@agrianalyze thank you sir also how to do d square analysis

@BAJRANGKUSRO 3 года назад

Sir how to install r studio

@agrianalyze 3 года назад

First install R in your system followed by Rstudio. cran.r-project.org/bin/windows/base/ www.rstudio.com/products/rstudio/download/

@BAJRANGKUSRO 3 года назад

Sir r studio download but package are not working

@BAJRANGKUSRO 3 года назад

Thankyou so much sir given information 😊😊

@BAJRANGKUSRO 3 года назад

Sir how to result exported to excel file par video banaiye sir

@agrianalyze 3 года назад

For sure ! Thank you for your suggestion. You can export using write.xlsx() from xlsx package.

@MrOgunsanya 2 года назад

You need to check the formula for heritability in the package. Heritability doesn't come out right.

@agrianalyze 2 года назад

Thank you for the suggestions. I will look into it! Regards Raj

@MrOgunsanya 2 года назад

@@agrianalyze the error term component that makes up the phenotypic variance should be devided by the number of replications.

@botanyresearchsolutions4849 3 года назад

reply me soon plz

@gopikrishangaur1867 2 года назад

For d2 analysis contact me.

@agrianalyze 3 года назад

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