loading data using dartR

[Will Purser]

Hey guys, I've been trying to run the dartR package and seem to be running into some issues. I'm trying to load some SNP data from Diversity Arrays and it keeps coming up with an error message. It'd be great if someone could please give me some insight into what the issue is, or how I might go about fixing it Thanks in advance!

Error Message:

Error in file(file, "rt") : cannot open the connection

[Dale Maschette]

Hi Will,
Can you post the code that is producing the error as well? That error is usually filepath related.

-Dale

Sent from the village hidden in the leaves

[Arthur Georges]

I agree with Dale. RStudio is looking in the wrong place for the file. Maybe check your setwd statement.

A

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[Will Purser]

Hey Guys, thanks for the quick response. I'll copied the code below (up until where I'm encountering the error message).

rm(list=ls())

install.packages("devtools")
library(devtools)
install_github("green-striped-gecko/dartR")
library(dartR)


# Create a directory, place the sample files in it, and point to it.

#where the original data is stored
data = "~/cloudstor/Litoria_rubella/01_original_data/genetic/Report-DLit20-5353/"
#where you want all the analyses to output
home = "~/cloudstor/Litoria_rubella/02_genetic/01_structure/"
#set directory to the data folder location
setwd("C:/Users/Willis/cloudstor/Shared/Litoria_rubella/01_original_data/genetic/Report-DLit20-5353")


# Read in the data and assign the individual metadata.
  gl <- gl.read.dart(filename = "Report_DLit20-5353_SNP_mapping_2.csv", ind.metafile = "~/cloudstor/Litoria_rubella/01_original_data/genetic/metadata/rubella_locations.csv")

[Bernd.Gruber]

Hi,

 

Can you try to copy your data locally and then run the function.

 

Though in principal why that should not work if the files are in you specified cloudstore folders.

 

If you want to check you can write:

 

dir() # here you should see your Report_DLit20-5353_SNP_mapping_2.csv file (as you used to set via setwd())

 

and via

 

dir("~/cloudstor/Litoria_rubella/01_original_data/genetic/metadata/”)

 

you should see your ind.meta file

 

 

Maybe easier to copy you ind.metafile into the folder where your dart report is to make sure R can find it.

 

Hope that helps,

 

Bernd

 

 

 

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