search

NESCent / popgenInfo

Vignettes for Population Genetics in R
http://popgen.nescent.org
MIT License
20 stars 50 forks source link

Vignette illustrating the use of the package R.SamBada #215

Open SolangeD opened 5 years ago

SolangeD commented 5 years ago

This vignette illustrates the use of the package R.SamBada to detect potential signature of selection using a correlative approach between gentoype and envrionmental conditions

hlapp commented 5 years ago

@SolangeD many thanks for your submission! We're looking into the reason(s) for the build failure.

hlapp commented 5 years ago

Build failure is outside of this vignette: #216. (For now, that is.)

hlapp commented 5 years ago

Build succeeds now. Nice work @SolangeD!. Do you and/or @zkamvar have suggestions for who would be good reviewers?

smanel commented 5 years ago

Suggestion of reviewer: Brenna.Forester@colostate.edu

hlapp commented 5 years ago

@BrennaF would you be available to review as per @smanel's suggestion?

Could anyone suggest a second reviewer?

smanel commented 5 years ago

I can try to do it.

BrennaF commented 5 years ago

Hi all - I can also review, but will need a little time (a week?) since we're busy getting ready for our field season.

hlapp commented 5 years ago

@BrennaF and @smanel thank you so much! If you need more time I think that's totally fine.

smanel commented 5 years ago

Can you tell me where I can edit and test the vignette. I cannot edit it when I go on the above link.

smanel commented 5 years ago

And for mac? Perhaps better to say that : For unix, replace "windows" by "unix", and for mac by ???

GDS file (format from SNPRelate package). The file is different for windows or unix user (created with prepareGeno)

if(Sys.info()['sysname']=='Windows'){ gdsFile=system.file("extdata", "uganda-subset-mol_windows.gds", package = "R.SamBada") #If you run Windows }else{ gdsFile=system.file("extdata", "uganda-subset-mol_unix.gds", package = "R.SamBada") #If you run MacOS or Linux }

smanel commented 5 years ago

Oups the information is already given. No change to add.

smanel commented 5 years ago

l41:I do not understand l41 "#Plink ped input file" l129: an error in "environment" l150: remove s to "examples" l151: "We can delete correlated variables that are above a given correlation threshold" -->Correlated variables can be removed following the chosen threshold l151:" Check if there is a population structure to include it as an "environmental variable" in your environmental file". Not sure to see whith which option

smanel commented 5 years ago

l142: an error message :

createEnv(locationFileName=locationFile, outputFile='uganda-subset-env.csv', x='longitude',y='latitude',locationProj=4326,separator=';', worldclim=TRUE, saveDownload=TRUE, rasterName=NULL,rasterProj=NULL, interactiveChecks=FALSE) #Also try with interactiveChecks=TRUE [1] "loading location file" [1] "Downloading variables from Worldclim database" essai de l'URL 'https://biogeo.ucdavis.edu/data/climate/worldclim/1_4/tiles/cur/bio_27.zip' Content type 'application/zip' length 70216984 bytes (67.0 MB)

downloaded 67.0 MB

essai de l'URL 'https://biogeo.ucdavis.edu/data/climate/worldclim/1_4/tiles/cur/tmin_27.zip' Content type 'application/zip' length 49442777 bytes (47.2 MB)

downloaded 47.2 MB

essai de l'URL 'https://biogeo.ucdavis.edu/data/climate/worldclim/1_4/tiles/cur/tmax_27.zip' Content type 'application/zip' length 48859678 bytes (46.6 MB)

downloaded 46.6 MB

essai de l'URL 'https://biogeo.ucdavis.edu/data/climate/worldclim/1_4/tiles/cur/prec_27.zip' Content type 'application/zip' length 18820116 bytes (17.9 MB)

downloaded 17.9 MB

Error in .local(.Object, ...) :

De plus : There were 50 or more warnings (use warnings() to see the first 50) Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer", : Cannot create a RasterLayer object from this file. (file does not exist)

SolangeD commented 5 years ago

Hi,

regarding the problem with createEnv, could I have the output of warnings() (after running the command line) to identify the problem?

Many thanks in advance

solange

De : Stéphanie Manel notifications@github.com Envoyé : mardi, 4 juin 2019 14:51:39 À : NESCent/popgenInfo Cc : Duruz Solange; Mention Objet : Re: [NESCent/popgenInfo] Vignette illustrating the use of the package R.SamBada (#215)

l142: an error message :

createEnv(locationFileName=locationFile, outputFile='uganda-subset-env.csv', x='longitude',y='latitude',locationProj=4326,separator=';', worldclim=TRUE, saveDownload=TRUE, rasterName=NULL,rasterProj=NULL, interactiveChecks=FALSE) #Also try with interactiveChecks=TRUE [1] "loading location file" [1] "Downloading variables from Worldclim database" essai de l'URL 'https://biogeo.ucdavis.edu/data/climate/worldclim/1_4/tiles/cur/bio_27.zip' Content type 'application/zip' length 70216984 bytes (67.0 MB)

downloaded 67.0 MB

essai de l'URL 'https://biogeo.ucdavis.edu/data/climate/worldclim/1_4/tiles/cur/tmin_27.zip' Content type 'application/zip' length 49442777 bytes (47.2 MB)

downloaded 47.2 MB

essai de l'URL 'https://biogeo.ucdavis.edu/data/climate/worldclim/1_4/tiles/cur/tmax_27.zip' Content type 'application/zip' length 48859678 bytes (46.6 MB)

downloaded 46.6 MB

essai de l'URL 'https://biogeo.ucdavis.edu/data/climate/worldclim/1_4/tiles/cur/prec_27.zip' Content type 'application/zip' length 18820116 bytes (17.9 MB)

downloaded 17.9 MB

Error in .local(.Object, ...) :

De plus : There were 50 or more warnings (use warnings() to see the first 50) Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer", : Cannot create a RasterLayer object from this file. (file does not exist)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/NESCent/popgenInfo/pull/215?email_source=notifications&email_token=AFR26WQPH5TYRTUNSHYAF2LPYZQNXA5CNFSM4HMBI5LKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODW4OXBA#issuecomment-498658180, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFR26WQXBVJW5FTC7STNZYLPYZQNXANCNFSM4HMBI5LA.

smanel commented 5 years ago

like a problem with gdal?

createEnv(locationFileName=locationFile, outputFile='uganda-subset-env.csv', x='longitude',y='latitude',locationProj=4326,separator=';', worldclim=TRUE, saveDownload=TRUE, rasterName=NULL,rasterProj=NULL, interactiveChecks=FALSE) #Also try with interactiveChecks=TRUE [1] "loading location file" [1] "Downloading variables from Worldclim database" Error in .local(.Object, ...) :

De plus : There were 50 or more warnings (use warnings() to see the first 50) Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer", : Cannot create a RasterLayer object from this file. (file does not exist)

warnings()... Erreur : unexpected symbol in "warnings()..." warnings() Messages d'avis : 1: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

  • www.gdal.org (no HDF4 support!)
  • www.trac.osgeo.org/osgeo4w/ (with HDF4 support RECOMMENDED)
  • www.fwtools.maptools.org (with HDF4 support)

2: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 3: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

4: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 5: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

6: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 7: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

8: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 9: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

10: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 11: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

12: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 13: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

14: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 15: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

16: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 17: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

18: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 19: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

20: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 21: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

22: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 23: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

24: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 25: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

26: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 27: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

28: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 29: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

30: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 31: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

32: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 33: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

34: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 35: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

36: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 37: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

38: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 39: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

40: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 41: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

42: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 43: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

44: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 45: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

46: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 47: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

48: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 49: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

50: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE)

SolangeD commented 5 years ago

Hi,

yes it is definitely a problem with gdal installation.

The createEnv function relies on rgdal which requires gdal to be installed.

To install rgdal, please first remove it from the r library folder and then try the following

https://www.r-bloggers.com/installing-rgdal-on-a-mac/

Please let me know if it works

I'm surprised that the function behaved this way though. The presence of the rgdal package is checked at the beginning of the function. I will have to add a note in the documentation

De : Stéphanie Manel notifications@github.com Envoyé : mercredi, 5 juin 2019 13:10:10 À : NESCent/popgenInfo Cc : Duruz Solange; Mention Objet : Re: [NESCent/popgenInfo] Vignette illustrating the use of the package R.SamBada (#215)

like a problem with gdal?

createEnv(locationFileName=locationFile, outputFile='uganda-subset-env.csv', x='longitude',y='latitude',locationProj=4326,separator=';', worldclim=TRUE, saveDownload=TRUE, rasterName=NULL,rasterProj=NULL, interactiveChecks=FALSE) #Also try with interactiveChecks=TRUE [1] "loading location file" [1] "Downloading variables from Worldclim database" Error in .local(.Object, ...) :

De plus : There were 50 or more warnings (use warnings() to see the first 50) Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer", : Cannot create a RasterLayer object from this file. (file does not exist)

warnings()... Erreur : unexpected symbol in "warnings()..." warnings() Messages d'avis : 1: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

2: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 3: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

4: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 5: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

6: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 7: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

8: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 9: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

10: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 11: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

12: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 13: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

14: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 15: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

16: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 17: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

18: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 19: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

20: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 21: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

22: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 23: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

24: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 25: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

26: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 27: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

28: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 29: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

30: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 31: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

32: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 33: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

34: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 35: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

36: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 37: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

38: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 39: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

40: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 41: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

42: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 43: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

44: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 45: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

46: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 47: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

48: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE) 49: In gdal_setInstallation() : No GDAL installation found. Please install 'gdal' before continuing:

50: In gdal_setInstallation() : If you think GDAL is installed, please run: gdal_setInstallation(ignore.full_scan=FALSE)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/NESCent/popgenInfo/pull/215?email_source=notifications&email_token=AFR26WSGKBJ5OTXHPMILOCDPY6NJFA5CNFSM4HMBI5LKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODW7MCLA#issuecomment-499040556, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFR26WTBD33M5QOQFUJPVSDPY6NJFANCNFSM4HMBI5LA.

smanel commented 5 years ago

It does not work (installation of rgdal): I have the following error message

install.packages("rgdal",repos="http://www.stats.ox.ac.uk/pub/RWin") Warning in install.packages : package ‘rgdal’ is not available (for R version 3.5.1) Warning in install.packages : unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/el-capitan/contrib/3.5: impossible d'ouvrir l'URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/el-capitan/contrib/3.5/PACKAGES'

library(rgdal)-->I assume that it install the R package already on my computer? With this package I still have the previous error messagae

SolangeD commented 5 years ago

In that case you will have to follow the second option (named hard way) of the link I sent you

De : Stéphanie Manel notifications@github.com Envoyé : mercredi, 5 juin 2019 20:50:25 À : NESCent/popgenInfo Cc : Duruz Solange; Mention Objet : Re: [NESCent/popgenInfo] Vignette illustrating the use of the package R.SamBada (#215)

It does not work (installation of rgdal): I have the following error message

install.packages("rgdal",repos="http://www.stats.ox.ac.uk/pub/RWin") Warning in install.packages : package ‘rgdal’ is not available (for R version 3.5.1) Warning in install.packages : unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/el-capitan/contrib/3.5: impossible d'ouvrir l'URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/el-capitan/contrib/3.5/PACKAGES'

library(rgdal)-->I assume that it install the R package already on my computer? With this package I still have the previous error messagae

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/NESCent/popgenInfo/pull/215?email_source=notifications&email_token=AFR26WV6K5PIKYNOPBHOLBLPZADHDA5CNFSM4HMBI5LKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXAVISQ#issuecomment-499209290, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFR26WWHHP65MTCXMQCUXJLPZADHDANCNFSM4HMBI5LA.

smanel commented 5 years ago

1-I finally move on windows 10 (Rstudio, R 3.6). It works. I just noted that the package biomaRt is necessary to use the function PlotResultInteractive. I suggest to add a note in that give that this package should be installed with bioconductor.
2-I do not spend more time in working on Mac (Os) : It remains two problems at the moment : the version of the C compilator (gcc 7) and installation of rgdal.
So at the moment R. sambada is not working on "my" mac. But I did not try the suggestion.

BrennaF commented 5 years ago

Hello all - my apologies for the delay. I've just started running the tutorial, and I keep getting hung up on the prepareGeno call:

prepareGeno(fileName=genoFile,outputFile='uganda-subset-mol.csv',saveGDS=TRUE,mafThresh=0.05, missingnessThresh=0.1,interactiveChecks=FALSE) #Also try with interactiveChecks=TRUE

Rstudio just hangs when I run this. I've been waiting for 10 minutes currently. I tried restarting R, but it is currently doing the same thing...I'm assuming it shouldn't take that long. I'm on a windows machine using R v. 3.5.3. No errors or other problems in the set up code prior to this point...

BrennaF commented 4 years ago

Hello - the prepareGeno is now working for me - not sure what the problem was originally.

A few comments/suggestions on the vignette:

General comments:

The visualizations are fantastic! Looking forward to using this with my own data. Brenna

SolangeD commented 4 years ago

Hi Brenna,

Thank you very much for the reviewing of the vignette and for the useful comments you provided. I'm sorry for the very late answer, I was very busy these last few months and the corona crisis didn't help!

Based on your comments, a new version of the vignette has been pushed and a new version of R.SamBada has been released (version 0.1.2, available in the CRAN).

Here are my answers to your comment

* Line 124: I did not have the "uganda-subset-id.csv" file in my current directory to upload in the setLocation() browser window. Can you please add it?

The file is now copied in the working directory in section 1

* Line 142: createEnv() also failed for me with the same error that Stephanie got. I installed the rgdal package but I still had the same error (I'm using windows). It seems that gdal is a dependency for rgdal - can you provide instructions for installation?

Yes, gdal is indeed a dependency of rgdal, which in turn is a dependency of R.SamBada. Installation information for all OS is now given in the prerequisite function

* Line 163: remove this comment or make it more descriptive, since prepareEnv() as parameterized here is doing more than storing PC scores. Also, how does prepareEnv() determine which of a set of highly correlated variables will be removed? Is it random? If so, you should be clear about that since users may prefer to prune variables based on ecological/biological relevance.

the comment has been changed. Furthermore, the documentation of prepareEnv() has been updated, so as to specify that if two variables are more correlated than the defined threshold, then the first variable (order of appearance in the header of the environental file) will be kept while the other will be removed

* Line 206: What are these two plots that are produced? The description in prepareOutput() is minimal. Are these plots something users should be interpreting?

The documentation of prepareOutput has been updated to inform users on these graphs

* Line 211: typo - "interesting"

Typo corrected

* Line 245: "Error: Package "biomaRt" needed for this function to work. Please install it." Installed with bioconductor & then had to update rlang as well (and restart R and the tutorial) - might be best to include these in the dependencies at the start.

"SNPRelate" and "biomaRt" installation is now included at the beginning of the vignette

* Line 245: Great shiny app! How do you get the map to plot using the varnev (mine would only plot using the "pops" scale)? Also a y-axis label on the boxplot would be helpful.

The documentation of the plotInteractive has been updated to explain how to plot the varenv (need to check/uncheck layers on the right of your plot). The y-axis label has been added

* Line 272: I don't understand "presence/absence" for SNPs - how is it handling heterozygotes?

Sambada works on genotype not on SNP. As an example, here we plot Hapmap28985-BTA-73836_GG, so alleles GG for the SNP Hapmap28985-BTA-73836. If an individual has alleles GG then the genotype is present. Any other combination will return absent General comments:

* It might be useful to let users know if there are informative/interesting SNPs in the data set or not. For example, which SNPs are you confident are neutral vs. under selection? Then users could see how testing parameters differ, so that they'll be better able to interpret results when they see them for their own data.

A note has been added at the end of the vignette

* I also wasn't sure where test statistics from the GLM are reported...which SNPs are candidates based on what cutoff? The Manhattan plot is nice for visualization and inspection, but where are the qvalues and pvalues reported? Where is the FDR set? Are GIFs and p-value distributions provided anywhere to assess whether we're close to meeting the reported FDR?

The p and q-values are reported in prep$sambadaOutput. The q-values are calculated using Storey method and the pi0 (parameter needed to set the FDR) is shown in the p-value distribution graphs plotted when interactiveChecks=TRUE (as you asked, I added a comment in the documentation about these graphs). Note that given the limited number of SNPs in the dataset, these graphs look different from what we are used to, so that you probably haven't recognized them when plotted.

Again, thanks for the detailed review! Best, Solange

De : Brenna Forester notifications@github.com Envoyé : mardi, 22 octobre 2019 19:59 À : NESCent/popgenInfo Cc : Duruz Solange; Mention Objet : Re: [NESCent/popgenInfo] Vignette illustrating the use of the package R.SamBada (#215)

Hello - the prepareGeno is now working for me - not sure what the problem was originally.

A few comments/suggestions on the vignette:

General comments:

The visualizations are fantastic! Looking forward to using this with my own data. Brenna

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/NESCent/popgenInfo/pull/215?email_source=notifications&email_token=AFR26WX6LELRRHLQQXFIQ3TQP45RDA5CNFSM4HMBI5LKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEB6UVDY#issuecomment-545081999, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AFR26WX2OJQFXZCQFDE2SATQP45RDANCNFSM4HMBI5LA.