search

thibautjombart / adegenet

adegenet: a R package for the multivariate analysis of genetic markers
168 stars 64 forks source link

ade4 and adegenet #226

Closed GiselT closed 6 years ago

GiselT commented 6 years ago

hello, someone could help me I would like to work with a .csv file from genalex with SSR data .... but I can not call it correctly, I install the libraries. Could you explain how to do it? thank you very much

Gisel

thibautjombart commented 6 years ago

Hi Gisel, we can't help with such little info. We need a reproducible example if you want to report a bug. But this question sounds more like help you should seek from the adegenet forum: http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum

Note you need to subscribe if you don't want your post to be moderated.

GiselT commented 6 years ago

Dear, try to do it this way (excuse me but I'm new to R), I tried to call the file in different ways but I could not do it. 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)

**read.genalex(AN20pop.csv)

Error in readLines(genalex, n = 2) : object 'AN20pop.csv' not found

**

zkamvar commented 6 years ago

This question was cross-posted to the poppr forum and answered there: https://groups.google.com/d/msg/poppr/V30sA6mHAoQ/YkSu6eqSAgAJ

GiselT commented 6 years ago

thank you very much everyone for your help, now I will try, regards

Gisel

2018-02-27 12:11 GMT-03:00 Zhian N. Kamvar notifications@github.com:

This question was cross-posted to the poppr forum and answered there: https://groups.google.com/d/msg/poppr/V30sA6mHAoQ/YkSu6eqSAgAJ

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/thibautjombart/adegenet/issues/226#issuecomment-368910352, or mute the thread https://github.com/notifications/unsubscribe-auth/AjEFIu7qoJjSS7CUNFcrCaeVaxnzbpCWks5tZBs6gaJpZM4SUU3Q .

-- Lic. Gisel Taboada Becaria CONICET- Laboratorio de Biotecnología INTA- Estación Experimental Salta Ruta Nac. 68 Km 172 (4403) Cerrillos Salta - Argentina tel:+54-387-4902087/81