Asked by a user via email:

Hello,

I'm attempting to use the GWAStools package and unfortunately have not had much luck. I have a GDS object and would like to subset that GDS object for specific individuals, and then save the subsetted GDS object permanently in my directory. I'm attempting to use the gdsSubset function but do not know how to save the subsetted GDS file as a permanent file in my working directory. I would greatly appreciate any insight you may have.  I'm including my code below.

Thank you for your help,

Charlie Waters

# Create a new GDS file containing only the individuals for which we have phenotype and other meta data

# read in meta data for the individuals
sample_metadata <- read.csv("Scan_annotation_data_object.csv", header=T)

# First make vector of sample IDs
sampleIDs <- sample_metadata$scanID

# Write path to full GDS file. Not sure why it needs the path instead of the actual GDS object in R but oh well.
gdsfile <- "C:/Users/Waters/Dropbox (MERLAB)/Puerto_Rico_AD_GWAS/PR5geno.gds"

# Create temporary file...only way I can get the function to work
PR5geno_subset <- tempfile()

gdsSubset(gdsfile, PR5geno_subset, sample.include = sampleIDs)
gdsSubsetCheck(gdsfile, PR5_genofile_subset, sample.include = sampleIDs)

# Can't move forward. The example doesn&#39;t give any insight into how I can save the subset as a new GDS file.

I think Charlie was expecting gdsSubset to return a new GDS object that he/she can then save, but that is not how the function works. The second argument is the file name of the subsetted GDS file, which is already created by the function. In the example provided, PR5geno_subset contains a character string with the path to the new GDS file. Since it was assigned the output of tempfile(), that file is in the temporary directory. To create the subsetted file in the working directory instead, you would do the following:

newfile <- "PR5geno_subset.gds"
gdsSubset(gdsfile, newfile, sample.include = sampleIDs)