The GroupWrite method can be used to save simulation data sets to separate files for purposes beyond the scope of SEQPower. See below for more details:

spower show test GroupWrite

It will create 3 files for each group:

• A phenotype file with rows representing samples, the 1st column is sample name, the 2nd column is the quantitative or binary phenotype;
• A genotype file with rows representing variants and the columns represent sample genotypes (order of the rows matches the genotype file);
  • By default output are tab separated with each column being genotypes on two haplotypes; phase information is retained in the data, i.e., '10' and '01' are different phases
  • With --recode switch on, coding of genotypes are converted to minor allele counts (0/1/2). Missing values are denoted as NA
• A mapping file that matches the group ID and variant ID in pairs.

If multiple replicates are specified, as the example below, the output dataset will be named with replicate ID as part of file name suffix.

spower LOGIT KIT.gdat -a 1.5 --sample_size 2000 -P 0.8 --alpha 0.05 -v2 \
       --method "GroupWrite SimData" \
       -r 50 -j8

This command will result in files *_geno.txt, *_pheno.txt and *_mapping.txt recording simulated genotype, phenotype and variant map data.

With the --recode switch genotypes are recoded to minor allele counts:

spower LOGIT KIT.gdat -a 1.5 --sample_size 2000 -P 0.8 --alpha 0.05 -v2 \
       --method "GroupWrite SimData --recode" \
       -r 50 -j8