How to export data from Genalex .csv to R in poppr? I have SSR markers and diploid sp
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Gisel Taboada
Feb 27, 2018, 9:22:44 AM2/27/18
to poppr
Hello! Could Alguin help me? I am new to R and I am trying to anlay my data, but I still can not call the file in R .... install the libraries but I can not do it? somebody could help me. Thank you, thank you
install.packages("devtools")
install.packages("poppr", repos = "http://cloud.r-project.org/")
devtools::install_github("grunwaldlab/poppr")
library("poppr")
library("ade4")
library("adegenet")
x <- getfile(AN20pop.csv)
AN20 <- read.genalex(AN20pop.csv)
AN20
popdata <- poppr(AN20)
system.file("files/AN20pop.csv", package="poppr")
AN20pop <- read.genalex(system.file("files/AN20pop.csv", package="poppr"))
read.genalex(genalex, ploidy = 2, geo = FALSE, region = FALSE,
genclone = TRUE, sep = ",", recode = FALSE)
read.table(AN20pop.csv)
read.genalex(AN20pop.csv)
Zhian Kamvar
Feb 27, 2018, 10:10:18 AM2/27/18
to Gisel Taboada, poppr
Hello,
You should put quotes around the file name (assuming you are in the correct directory).
AN20 <- read.genalex("AN20pop.csv")
The reason this works is because putting quotes around the name tells R that it should interpret that part as a string of characters instead of a variable.
Note: his was also cross-posted on the adegenet help page: https://github.com/thibautjombart/adegenet/issues/226#issuecomment-368880005
Hope that helps,
Zhian
-----
Zhian N. Kamvar, Ph. D.
Postdoctoral Researcher (Everhart Lab)
Department of Plant Pathology
University of Nebraska-Lincoln
ORCID: 0000-0003-1458-7108
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Gisel Taboada
Feb 27, 2018, 10:19:37 AM2/27/18
to poppr
So in this way, would it be correct?
install.packages ( "devtools")
install.packages ( "poppr", repos = " http://cloud.r-project.org/ ")
devtools :: install_github ( "grunwaldlab / poppr")
biblioteca ( "poppr")
biblioteca ( "ade4")
biblioteca ( "adegenet")
x <- getfile (AN20pop.csv)
AN20 <- read.genalex ("AN20pop.csv")
AN20
popdata <- poppr (AN20)
system.file ( "archivos / AN20pop.csv", paquete = "poppr")
AN20pop <- read.genalex (system.file ( "archivos / AN20pop.csv", paquete = "poppr"))
read.genalex (GenAlEx, ploidía = 2, geo = FALSE, región = FALSE,
genclone = TRUE, sep = "", recode = FALSE)
read.table (AN20pop.csv)
read.genalex (AN20pop.csv)
Zhian Kamvar
Feb 27, 2018, 10:38:43 AM2/27/18
to Gisel Taboada, poppr
Hello,
Almost! For the code you present, you really only need four lines. I've added comments after the code that describes what it's doing.
biblioteca("poppr") # load poppr into your workspace
AN20 <- read.genalex("AN20pop.csv") # read the file called AN20pop.csv into the object called AN20
AN20 # view the contents of AN20 (should be a genclone object)
popdata <- poppr(AN20) # create a diversity table from your data
As you are a beginner, I would recommend using RStudio projects as well (https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects).
That should be it! You can perform all of you analyses using the AN20 object.
Hope that helps,
Zhian
P.S.
I want to make a note of a couple of things here to help encourage best practices:
1. getfile() allows you to browse for your files, but it's not very good for reproducible practices because you have to interactively run it.
2. system.file() is only for example data files. This is a common mis-conception because it's named terribly. A better replacement is file.path().
3. I see that you are installing from github. This may be risky because that is a development version. It's better to use install.packages() with CRAN.
-----
Zhian N. Kamvar, Ph. D.
Postdoctoral Researcher (Everhart Lab)
Department of Plant Pathology
University of Nebraska-Lincoln
ORCID: 0000-0003-1458-7108
To view this discussion on the web visit https://groups.google.com/d/msgid/poppr/e098a8f0-3d8c-45de-8118-08c9b1272796%40googlegroups.com.
Gisel Taboada
Mar 1, 2018, 10:31:28 AM3/1/18
to poppr
Dear Zhian
I was finally able to upload the file from readgenalex to poppr
gi <- read.genalex("C:/Users/Usuario/Desktop/R_example/AN20pop.csv", ploidy = 2, geo = FALSE, region = FALSE,
genclone = FALSE, sep = ",", recode = FALSE)
gi
gi@type
gi@tab
data("gi")
(pinflt <- locus_table(gi))
info_table(gi, type = "missing", plot = TRUE)
but now when I run the function
gi
/// GENIND OBJECT /////////
// 96 individuals; 17 loci; 170 alleles; size: 102.7 Kb
// Basic content
@tab: 96 x 170 matrix of allele counts
@loc.n.all: number of alleles per locus (range: 4-24)
@loc.fac: locus factor for the 170 columns of @tab
@all.names: list of allele names for each locus
@ploidy: ploidy of each individual (range: 2-2)
@type: codom
@call: read.genalex(genalex = "AN20pop.csv", ploidy = 2, geo = FALSE,
region = FALSE, genclone = FALSE, sep = ",", recode = FALSE)
// Optional content
@pop: population of each individual (group size range: 4-5)
@strata: a data frame with 1 columns ( Pop )
> gi@type
[1] "codom"
> gi@tab
PVag003.186 PVag003.187 PVag003.185 PVag003.181 BMd20.146 BMd20.185 BMd20.186
1 2 0 0 0 2 0 0
2 2 0 0 0 1 1 0
3 2 0 0 0 2 0 0
4 2 0 0 0 2 0 0
5 2 0 0 0 2 0 0
BMd20.184 BMd20.144 BMd41.270 BMd41.167 BMd41.259 BMd41.258 BMd41.267 BMd41.261
1 0 0 2 0 0 0 0 0
2 0 0 2 0 0 0 0 0
3 0 0 2 0 0 0 0 0
4 0 0 2 0 0 0 0 0
5 0 0 2 0 0 0 0 0
BMd42.174 BMd42.175 BMd42.176 BMd42.177 BMd42.183 BMd42.180 BMd42.178 BMd42.179
1 2 0 0 0 0 0 0 0
2 2 0 0 0 0 0 0 0
3 2 0 0 0 0 0 0 0
4 2 0 0 0 0 0 0 0
5 2 0 0 0 0 0 0 0
BMd42.149 BM172.107 BM172.99 BM172.132 BM172.117 BM172.130 BM172.109 BM172.113
1 0 2 0 0 0 0 0 0
2 0 2 0 0 0 0 0 0
3 0 2 0 0 0 0 0 0
4 0 2 0 0 0 0 0 0
5 0 2 0 0 0 0 0 0
BM172.112 BM172.111 BM172.120 BM172.119 BM172.134 BM172.100 BM143.150 BM143.154
1 0 0 0 0 0 0 2 0
2 0 0 0 0 0 0 0 2
3 0 0 0 0 0 0 2 0
4 0 0 0 0 0 0 0 2
5 0 0 0 0 0 0 2 0
BM143.137 BM143.148 BM143.147 BM143.144 BM143.155 BM143.133 BM143.132 BM143.166
1 0 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0 0
3 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0
5 0 0 0 0 0 0 0 0
BM143.151 BM143.160 BM143.161 BM143.172 BM143.180 BM143.182 BM143.157 BM143.169
1 0 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0 0
3 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0
5 0 0 0 0 0 0 0 0
BM143.149 BM143.159 BM143.165 BM143.186 BM143.146 BM143.143 BM210.183 BM210.189
1 0 0 0 0 0 0 2 0
2 0 0 0 0 0 0 0 2
3 0 0 0 0 0 0 2 0
4 0 0 0 0 0 0 NA NA
5 0 0 0 0 0 0 2 0
BM210.185 BM210.181 BM210.186 BM210.190 BM210.184 BM210.182 BM210.188 BM210.187
1 0 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0 0
3 0 0 0 0 0 0 0 0
4 NA NA NA NA NA NA NA NA
5 0 0 0 0 0 0 0 0
BM210.199 BM210.198 BMd37.148 BMd37.150 BMd37.154 BMd37.156 PVctt001.182
1 0 0 2 0 0 0 2
2 0 0 2 0 0 0 2
3 0 0 2 0 0 0 2
4 NA NA 2 0 0 0 0
5 0 0 2 0 0 0 0
PVctt001.172 PVctt001.183 PVctt001.181 PVctt001.175 BM151.166 BM151.164 BM151.168
1 0 0 0 0 2 0 0
2 0 0 0 0 2 0 0
3 0 0 0 0 2 0 0
4 2 0 0 0 2 0 0
5 2 0 0 0 2 0 0
BM151.182 BM151.172 BM151.173 BM151.176 BM188.172 BM188.192 BM188.200 BM188.177
1 0 0 0 0 2 0 0 0
2 0 0 0 0 2 0 0 0
3 0 0 0 0 2 0 0 0
4 0 0 0 0 2 0 0 0
5 0 0 0 0 2 0 0 0
BM188.174 PVag001.179 PVag001.172 PVag001.178 PVag001.175 PVag001.176 PVag001.171
1 0 2 0 0 0 0 0
2 0 0 2 0 0 0 0
3 0 0 0 2 0 0 0
4 0 0 2 0 0 0 0
5 0 0 0 2 0 0 0
PVag001.169 PVag001.168 GATS91.256 GATS91.247 GATS91.257 GATS91.245 GATS91.264
1 0 0 2 0 0 0 0
2 0 0 0 2 0 0 0
3 0 0 2 0 0 0 0
4 0 0 0 2 0 0 0
5 0 0 0 0 2 0 0
GATS91.268 GATS91.260 GATS91.253 GATS91.251 GATS91.243 GATS91.250 GATS91.224
1 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0
3 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0
5 0 0 0 0 0 0 0
GATS91.269 GATS91.271 GATS91.229 GATS91.249 GATS91.241 GATS91.240 GATS91.233
1 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0
3 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0
5 0 0 0 0 0 0 0
GATS91.232 BMd1.187 BMd1.186 BMd1.189 BMd1.183 BMd1.182 BMd1.195 BMd1.181 BMd1.185
1 0 2 0 0 0 0 0 0 0
2 0 2 0 0 0 0 0 0 0
3 0 2 0 0 0 0 0 0 0
4 0 2 0 0 0 0 0 0 0
5 0 2 0 0 0 0 0 0 0
BMd1.193 BMd1.286 BM157.135 BM157.134 BM157.130 BM157.133 BM157.132 BM157.116
1 0 0 2 0 0 0 0 0
2 0 0 2 0 0 0 0 0
3 0 0 0 2 0 0 0 0
4 0 0 0 2 0 0 0 0
5 0 0 0 2 0 0 0 0
BM157.115 BM157.121 BM157.127 BM157.128 BM157.129 BM157.124 BM157.150 BM157.131
1 0 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0 0
3 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0
5 0 0 0 0 0 0 0 0
BM157.162 BM157.160 BM157.157 BM157.141 BM157.144 PVat007.224 PVat007.225
1 0 0 0 0 0 2 0
2 0 0 0 0 0 2 0
3 0 0 0 0 0 2 0
4 0 0 0 0 0 2 0
5 0 0 0 0 0 2 0
PVat007.207 PVat007.223 PVat007.221 PVat007.231 PVat007.211 PVat007.279
1 0 0 0 0 0 0
2 0 0 0 0 0 0
3 0 0 0 0 0 0
4 0 0 0 0 0 0
5 0 0 0 0 0 0
PVat007.261 PVat007.237 PVat007.239 PVat007.257 BM201.125 BM201.124 BM201.126
1 0 0 0 0 2 0 0
2 0 0 0 0 2 0 0
3 0 0 0 0 2 0 0
4 0 0 0 0 2 0 0
5 0 0 0 0 2 0 0
BM201.129 BM201.123 BM201.122 BM201.150
1 0 0 0 0
2 0 0 0 0
3 0 0 0 0
4 0 0 0 0
5 0 0 0 0
[ reached getOption("max.print") -- omitted 91 rows ]
I get this message, what does it mean? Did not the data go well? I do not take them as codomintantes markers in a dipliode species?
Thanks, I hope you can help me.
Gi
Zhian Kamvar
Mar 1, 2018, 10:43:55 AM3/1/18
to Gisel Taboada, poppr
Hi Gisel,
[ reached getOption("max.print") -- omitted 91 rows ]
I get this message, what does it mean? Did not the data go well? I do not take them as codomintantes markers in a dipliode species?Thanks, I hope you can help me.
There's no error here. This is R telling you that it won't print out your entire data set to the screen because it's too big, but this is not something to worry about; your data is still there.
In the future, it's usually a good idea to copy and paste the error message (and only the error message) into a search engine to see if anyone else has found the answer.
Additionally, if you want to access the components of a genind object, it's not a good idea to use the `@` operator. Instead, use the accessors (like tab() and nInd()) as detailed in the adegenet basics tutorial: https://github.com/thibautjombart/adegenet/blob/master/tutorials/tutorial-basics.pdf
Best,
Zhian
-----
Zhian N. Kamvar, Ph. D.
Postdoctoral Researcher (Everhart Lab)
Department of Plant Pathology
University of Nebraska-Lincoln
ORCID: 0000-0003-1458-7108
To view this discussion on the web visit https://groups.google.com/d/msgid/poppr/673cc3db-81d7-4461-881f-fb0fd210d51d%40googlegroups.com.
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