Popgenome R package

Question

[yp]

Hello,

I would like to use Popgenome R package to calculate diversity stats. I have a SNP data in the HapMap format. I used following R code to upload hap map file, but getting an error. The GFF file is in the same folder.

GENOME.class<-readHapMap("popgenome/test_631.hmp",populations=FALSE,outgroup=FALSE,gffpath="test_631.gff")

Error in readHapMap("popgenome/test_631.hmp", populations = FALSE, outgroup = FALSE, : unused argument (gffpath = "test_631.gff")

Do I need to use to tabix index file for hapmap and gff file?

Thanks, yp

Answer 1

[goodez]

I checked the documentation and there is no gffpath argument. Instead use hap_gffpath

Here is the docs for PopGenome if it helps: PopGenome

Answer 2

[yp]

Thanks for your reply.

I changed it to hap_gffpath, but it didn't work.

GENOME.class <- readHapMap("popgenome/",hap_gffpath="popgenome/",populations=FALSE,outgroup=FALSE)

Error in if (file == "") file <- stdin() else { : missing value where TRUE/FALSE needed

Could you please share an example hapmap file and codes?

Thanks, yp

[goodez]

No problem. Next time just add a comment to my answer though, rather than a separate answer.

Can you post the results of list.files("popgenome/")

[yp]

it is printing 0.

list.files("popgenome/") character(0)

[goodez]

I'm assuming you have a folder somewhere called "popgenome" which contains the relevant files?

You need to use setwd(path/to/folder/above/popgenome). Don't set it to "popgenome", but set it to the folder which contains "popgenome".

[yp]

Yes, I have a popgenome folder, which has all the relevant files. I am setting the path to one level above.

Now, I moved HapMap and gff file to a separate folder- "hapmap/". list.file command is printing the file names

list.files("hapmap/") [1] "test_631.gff" "test_631.hmp"

Then, I use following code. But still not working.

GENOME.class <- readHapMap("hapmap/",hap_gffpath="hapmap/",populations=FALSE,outgroup=FALSE)

Error in if (file == "") file <- stdin() else { : missing value where TRUE/FALSE needed

Do you have an example hapmap file?

Thanks, yp

[goodez]

Sorry I don't work with these types of files. You can try readData("test_631.hmp", format="HapMap") to see if your file is good for importing. Also from the documentation, I think you need 2 separate folders. 1 folder (the first argument) is for input "files of different individuals for one chromosome". The 2nd folder (second argument) is for the HapMap GFF.

[goodez]

Also, you can find example data by doing this in R

here <- find.package("PopGenome")
setwd(paste0(here, "/data")))
# You are now set to the directory containing PopGenome test data
list.files()

[yp]

Thanks!

I tried two ways to load files into the Popgenome. But none of them is working for me.

1. VCF - I created VCF and GFF files for each chromosome and stored in a separate folder.

GENOME.class <- readData("chr_vcf/", format="VCF", gffpath="gff/chr_gff/",FAST = FALSE,include.unknown = TRUE)

It is aborting the R session.

1. Hapmap file format

GENOME.class<-readData("hapmap/", format="HapMap",populations = FALSE,outgroup = FALSE,gffpath ="gff/",include.unknown = TRUE) | : | : | 100 % | Read 321000 items

Error in CCC$matrix : $ operator is invalid for atomic vectors