error with vcf2pcadapt command

[fkatharina]

Dear Michael,

I wonder if you could help with an error I encounter using the pcadapt package?
I am following the manual to load vcf data into R, wanting to dentify outlier loci using the pcadapt command.

I first read the data into R using vcfR, as the manual suggests:
data <- read.vcfR("data.vcf")

However, when I then use the following command for conversion, I get an error message:
data_pcadapt <- vcf2pcadapt(data, output = "data.pcadapt", allele.sep = c("/", "|"))
Error in vcfR::read.vcfR(input, verbose = FALSE) : The parameter file is expected to be a character.

I have already browsed the web but cannot understand why it would not recognize the vcf file if I loaded it according to pcadapt-manual-instructions...?

Any advice you can provide would be greatly appreciated.

best regards,
Katharina

[Mary-00]

Hi,
I also recently use pcadapt (v 4.0.3), the below command works well and reads the vcf file:
vcf2pcadapt(data, output = "data.pcadapt", allele.sep = c("/", "|"))

Best

[fkatharina]

Hi Mary,
thanks for your reply. This is exactly the same command I am using, but I continuously get this error:
Error in vcfR::read.vcfR(input, verbose = FALSE) :
The parameter file is expected to be a character.

With which command did you load your vcf file into R?

I load it with vcfR and when doing this get a "large vcfR" object. Is this the same for you?

thanks ,
Katharina

[Mary-00]

I used just this command to load vcf to the package. Please try it without your first command.

Hope it helps

[privefl]

Note that you should not use vcf2pcadapt.
The correct way to use pcadapt (for any type of data, here vcf) is to use

filename <- read.pcadapt(path_to_vcf, type = "vcf")
x <- pcadapt(filename, K = 20) 

[Mary-00]

Hi Privefl,
I used that command to convert vcf file to pcadapt format based on the manual. then used
file2 <- read.pcadapt ("file.pcadapt", type="pcadapt") and other steps and get the results without error. however, my results are a bit strange that posted as an issue here.

[mblumuga]

@Mary-00 and @fkatharina, can you use the solution proposed by @privefl and tell us if it works.

[fkatharina]

just gave it a try and it works, many thanks to all and particularly to @privefl for the right solution!

[mblumuga]

Great, glad that it works.