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:
--recodeswitch on, coding of genotypes are converted to minor allele counts (0/1/2). Missing values are denoted as NA
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
*_mapping.txt recording simulated genotype, phenotype and variant map data.
--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