Genetic Variability and Association analysis in R

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  • Опубліковано 30 вер 2024

КОМЕНТАРІ • 140

  • @agrianalyze
    @agrianalyze  6 місяців тому +1

    Genotypic Correlation with interpretation and heat map
    ua-cam.com/video/FPRTDPXUz90/v-deo.html
    Phenotypic Correlation with interpretation and heat map
    ua-cam.com/video/kc2Nlp0GuPg/v-deo.html
    Phenotypic Path Analysis with interpretation
    ua-cam.com/video/3T5dQ77YgoI/v-deo.html
    Genotypic Path Analysis with interpretation
    ua-cam.com/video/KLTupZUVfic/v-deo.html
    Calculation of Genetic parameters like genetic advance, genetic advance as percentage of mean, heritability etc
    ua-cam.com/video/s_hRJOf8hww/v-deo.html

  • @agrianalyze
    @agrianalyze  3 роки тому +9

    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

  • @asmashaheen5372
    @asmashaheen5372 3 роки тому +9

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

  • @josephchavda4589
    @josephchavda4589 3 роки тому +8

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

    • @agrianalyze
      @agrianalyze  3 роки тому

      Thank you for this kind words🙏

  • @prasanthchigurupatii
    @prasanthchigurupatii 3 роки тому +3

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

    • @agrianalyze
      @agrianalyze  3 роки тому +4

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

    • @prasanthchigurupatii
      @prasanthchigurupatii 3 роки тому +2

      @@agrianalyzeThank you sir

  • @rtoolsforagriculturer-tag7675
    @rtoolsforagriculturer-tag7675 2 роки тому +1

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

    • @agrianalyze
      @agrianalyze  2 роки тому

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

  • @tayoolatunji7079
    @tayoolatunji7079 2 місяці тому +1

    Thank you

  • @muhammaduzair3659
    @muhammaduzair3659 3 роки тому +1

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

  • @agrianalyze
    @agrianalyze  3 роки тому +4

    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

  • @agriconceptlearning4153
    @agriconceptlearning4153 2 роки тому +1

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

  • @botanyresearchsolutions4849
    @botanyresearchsolutions4849 3 роки тому +2

    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
      @agrianalyze  3 роки тому +1

      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
      @botanyresearchsolutions4849 3 роки тому

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

    • @vaishnavikhode9178
      @vaishnavikhode9178 3 роки тому

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

  • @vaibhavchittora1579
    @vaibhavchittora1579 3 роки тому +2

    a very informative and good explanation for new R users

  • @shikhadubey2251
    @shikhadubey2251 2 роки тому +1

    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?

  • @SimranjitKaur-gb2vd
    @SimranjitKaur-gb2vd 3 роки тому +3

    Please bring PCA and regression analysis in R

  • @Rutvi_patel_1111
    @Rutvi_patel_1111 3 роки тому +2

    Very useful package. Thanks for sharing this video.

  • @niveditashettigar452
    @niveditashettigar452 3 роки тому +1

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

  • @tonmoychakrabarty2610
    @tonmoychakrabarty2610 3 роки тому +1

    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 {"

  • @gopikrishangaur1867
    @gopikrishangaur1867 2 роки тому

    For d2 analysis contact me.

  • @deepakkaushik6821
    @deepakkaushik6821 3 роки тому +2

    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
      @agrianalyze  3 роки тому +1

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

    • @vaibhavchittora1579
      @vaibhavchittora1579 3 роки тому

      go for augmentedRCBD package

    • @gazalaparveen3665
      @gazalaparveen3665 2 роки тому

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

  • @botanyresearchsolutions4849
    @botanyresearchsolutions4849 3 роки тому +1

    reply me soon plz

  • @Eshwar-zp6qf
    @Eshwar-zp6qf 2 роки тому +1

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

    • @agrianalyze
      @agrianalyze  2 роки тому

      Sorry I don't have idea about it

  • @shikhadubey2251
    @shikhadubey2251 3 роки тому +1

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

    • @agrianalyze
      @agrianalyze  3 роки тому +1

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

  • @Hxrold1493
    @Hxrold1493 2 роки тому +1

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

    • @agrianalyze
      @agrianalyze  2 роки тому +1

      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
      @Hxrold1493 2 роки тому

      @@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.

  • @ulixx63
    @ulixx63 3 роки тому +2

    Genotypes are hybrids or lines?

    • @agrianalyze
      @agrianalyze  3 роки тому +1

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

  • @sreenivasshrihaan1318
    @sreenivasshrihaan1318 3 роки тому +1

    IN R STUDIO WHICH PACKAGE IS SUITABLE FOR GENERATION MEAN ANALYSIS

    • @agrianalyze
      @agrianalyze  3 роки тому

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

  • @BAJRANGKUSRO
    @BAJRANGKUSRO 3 роки тому +1

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

    • @agrianalyze
      @agrianalyze  3 роки тому +2

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

  • @hiteshkumarsaini1529
    @hiteshkumarsaini1529 2 роки тому

    What is commend line for two year RBD ANALYSIS?

  • @MrOgunsanya
    @MrOgunsanya 3 роки тому +1

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

    • @agrianalyze
      @agrianalyze  3 роки тому +1

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

    • @MrOgunsanya
      @MrOgunsanya 3 роки тому

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

  • @vijayrajamanickam6847
    @vijayrajamanickam6847 Рік тому

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

  • @bhumikasinghlodhi6632
    @bhumikasinghlodhi6632 Рік тому

    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

  • @botanyresearchsolutions4849
    @botanyresearchsolutions4849 3 роки тому +1

    what is mean by NaNs in geno corr analysis

    • @agrianalyze
      @agrianalyze  3 роки тому +1

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

  • @hamzaashfaq4869
    @hamzaashfaq4869 3 роки тому +2

    How do we export the results in console to excel?

    • @agrianalyze
      @agrianalyze  3 роки тому +2

      use write.xlsx() function of xlsx package

    • @hamzaashfaq4869
      @hamzaashfaq4869 3 роки тому +2

      @@agrianalyze Worked!
      Thanks

    • @BAJRANGKUSRO
      @BAJRANGKUSRO 3 роки тому +1

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

    • @hamzaashfaq4869
      @hamzaashfaq4869 3 роки тому +1

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

  • @ranjeetwankhade6772
    @ranjeetwankhade6772 2 роки тому

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

  • @md.abusyed5635
    @md.abusyed5635 3 роки тому +1

    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
      @agrianalyze  2 роки тому

      Namaskar Abu
      Please refer augmented RCBD package.
      Regards
      RAJ

    • @md.abusyed5635
      @md.abusyed5635 2 роки тому

      @@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.

  • @gopikrishangaur1867
    @gopikrishangaur1867 3 роки тому +1

    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
      @agrianalyze  3 роки тому +1

      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
      @gopikrishangaur1867 3 роки тому +1

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

    • @Rin_Chawngthu
      @Rin_Chawngthu 2 роки тому +1

      D square analysis using Indostat

  • @shilpan.murthy2174
    @shilpan.murthy2174 Рік тому

    Wat is the codes for path analysis in augmented design

    • @agrianalyze
      @agrianalyze  Рік тому

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

  • @darshanraj1939
    @darshanraj1939 Рік тому

    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?

  • @purnadhanuk5713
    @purnadhanuk5713 3 роки тому +1

    sir will this script work for alpha lattice design?

    • @agrianalyze
      @agrianalyze  3 роки тому

      This function are made for RCBD

  • @cyrinerobbana1691
    @cyrinerobbana1691 7 місяців тому

    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
      @agrianalyze  7 місяців тому

      There is ppt in description box. You can use that

    • @cyrinerobbana1691
      @cyrinerobbana1691 7 місяців тому

      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.

  • @yaziegenet6551
    @yaziegenet6551 2 роки тому

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

  • @SimranjitKaur-gb2vd
    @SimranjitKaur-gb2vd 3 роки тому +1

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

  • @sweety-d1e
    @sweety-d1e Рік тому

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

  • @seenaamulatu3825
    @seenaamulatu3825 2 роки тому

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

  • @sanayakashyap6256
    @sanayakashyap6256 3 роки тому

    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

  • @botanyresearchsolutions4849
    @botanyresearchsolutions4849 3 роки тому

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

  • @s.husain6125
    @s.husain6125 2 роки тому

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

    • @agrianalyze
      @agrianalyze  2 роки тому

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

    • @s.husain6125
      @s.husain6125 2 роки тому

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

  • @truongphu7407
    @truongphu7407 Рік тому

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

  • @mayuribarai7624
    @mayuribarai7624 2 роки тому

    Please make a video on AMMI model for stability analysis

  • @diversityboys9602
    @diversityboys9602 2 роки тому

    how can we calculate phenotypic path analysis without replication

  • @rumitpatel6622
    @rumitpatel6622 3 роки тому +2

    Great sir

  • @SHUBHAMSINGH-gh6ln
    @SHUBHAMSINGH-gh6ln Рік тому

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

  • @asmashaheen5372
    @asmashaheen5372 3 роки тому

    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?

  • @BAJRANGKUSRO
    @BAJRANGKUSRO 3 роки тому +2

    Sir how to install r studio

    • @agrianalyze
      @agrianalyze  3 роки тому +1

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

    • @BAJRANGKUSRO
      @BAJRANGKUSRO 3 роки тому +1

      Sir r studio download but package are not working

    • @BAJRANGKUSRO
      @BAJRANGKUSRO 3 роки тому

      Thankyou so much sir given information 😊😊

  • @basazinewdegu4181
    @basazinewdegu4181 2 роки тому

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

  • @BAJRANGKUSRO
    @BAJRANGKUSRO 3 роки тому

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

  • @tarunreddybezawada6678
    @tarunreddybezawada6678 3 роки тому +1

    how can we draw path diagram in R

    • @agrianalyze
      @agrianalyze  3 роки тому

      Check the link of the pinned comment in this video

  • @yellankinaveen2496
    @yellankinaveen2496 2 роки тому

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

    • @agrianalyze
      @agrianalyze  2 роки тому

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

  • @nirija4158
    @nirija4158 2 роки тому

    Thanku so much... It helped me a lot

  • @prashanthyelimineti2468
    @prashanthyelimineti2468 3 роки тому

    Is their any packages for triallel and quadriallel analysis

  • @yellankinaveen2496
    @yellankinaveen2496 2 роки тому

    Error in `contrasts

  • @sushantgadge7580
    @sushantgadge7580 2 роки тому

    function gen.var is not available how to install

    • @agrianalyze
      @agrianalyze  2 роки тому

      Install and load variability package

    • @sushantgadge7580
      @sushantgadge7580 2 роки тому

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

  • @s.husain6125
    @s.husain6125 2 роки тому

    Can i use same procedure in pooled CRD sir

  • @evdivakarasastry
    @evdivakarasastry 3 роки тому

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

    • @agrianalyze
      @agrianalyze  3 роки тому +1

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

  • @shuyiyang3628
    @shuyiyang3628 3 роки тому +1

    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
      @agrianalyze  3 роки тому

      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
      @shuyiyang3628 3 роки тому +1

      @@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
      @agrianalyze  3 роки тому

      Sorry I didn't know about it!

    • @shuyiyang3628
      @shuyiyang3628 3 роки тому +1

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

  • @fikirteassefa7939
    @fikirteassefa7939 9 місяців тому

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

  • @faozyathaminou7699
    @faozyathaminou7699 3 роки тому

    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

  • @damotanteneh4360
    @damotanteneh4360 3 роки тому

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

  • @shabbirakhtar3662
    @shabbirakhtar3662 2 роки тому

    who to do cluster distance?

  • @getatube16
    @getatube16 2 роки тому

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

  • @tonmoychakrabarty2610
    @tonmoychakrabarty2610 3 роки тому

    Can we analyse the environmental correlation?

  • @prasadvadigeri4039
    @prasadvadigeri4039 3 роки тому

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

  • @jyothsna_jb
    @jyothsna_jb 2 роки тому

    Thank you very much, Sir

  • @monisham4277
    @monisham4277 Рік тому

    very useful sir thank u

  • @md.mukulmia4374
    @md.mukulmia4374 Рік тому

    Thanks a lot, good video.

  • @uttejkarla8749
    @uttejkarla8749 3 роки тому

    Sir, kindly make a video on AMMI analysis in R

  • @sachinbarad4331
    @sachinbarad4331 3 роки тому

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

    • @agrianalyze
      @agrianalyze  3 роки тому +1

      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

  • @md.shahriarkobir5191
    @md.shahriarkobir5191 2 роки тому

    Great work. Many many thanks

  • @asmashaheen5372
    @asmashaheen5372 3 роки тому +2

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

  • @poopingboy9637
    @poopingboy9637 3 роки тому +1

    Great, thanks very much