===== Write Simulation Data Set to Files =====
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:

<code bash>
spower show test GroupWrite
</code>\\
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.

==== Example ====
<code bash>
spower LOGIT KIT.gdat -a 1.5 --sample_size 2000 -P 0.8 --alpha 0.05 -v2 \
       --method "GroupWrite SimData" \
       -r 50 -j8
</code>\\
This command will result in files ''*_geno.txt'', ''*_pheno.txt'' and ''*_mapping.txt'' recording simulated genotype, phenotype and variant map data.

<hidden initialState="visible" -noprint>
<code text KIT_geno.txt>
KIT:55524145	00	00	00	00	00	00	00	00	00
KIT:55524161	00	00	00	00	00	00	00	00	00
KIT:55561658	00	00	00	00	00	00	00	00	00
KIT:55561805	00	00	00	00	00	00	00	00	00
KIT:55561861	00	00	00	00	00	00	00	00	00
KIT:55564614	00	00	00	00	00	00	00	00	00
KIT:55564616	00	00	00	00	00	00	00	00	00
KIT:55570043	00	00	00	00	00	00	00	00	00
KIT:55570067	00	00	00	00	00	00	00	00	00
KIT:55589871	00	00	00	00	00	00	00	00	00
KIT:55592059	00	00	00	00	00	00	00	00	00
KIT:55592061	00	00	00	00	00	00	00	00	00
KIT:55593551	00	00	00	00	00	00	00	00	00
KIT:55593560	00	00	00	00	00	00	00	00	00
KIT:55593608	00	00	00	00	00	00	00	00	00
KIT:55598029	00	00	00	00	00	00	00	00	00
KIT:55598065	00	00	00	00	00	00	00	00	00
...
</code>
</hidden>\\
<hidden initialState="visible" -noprint>
<code text KIT_pheno.txt>
SAMP1	1
SAMP2	1
SAMP3	1
SAMP4	1
...
SAMP1997	0
SAMP1998	0
SAMP1999	0
SAMP2000	0
</code>
</hidden>\\
<hidden initialState="visible" -noprint>
<code text KIT_mapping.txt>
KIT	KIT:55524145
KIT	KIT:55524161
KIT	KIT:55561658
KIT	KIT:55561805
KIT	KIT:55561861
KIT	KIT:55564614
KIT	KIT:55564616
KIT	KIT:55570043
KIT	KIT:55592061
...
</code>
</hidden>\\
=== Recode genotypes ===
With the ''%%--%%recode'' switch genotypes are recoded to minor allele counts:

<code bash>
spower LOGIT KIT.gdat -a 1.5 --sample_size 2000 -P 0.8 --alpha 0.05 -v2 \
       --method "GroupWrite SimData --recode" \
       -r 50 -j8
</code>\\
<hidden initialState="visible" -noprint>
<code text KIT_geno.txt>
KIT:55524145	0	0	0	0	0	0	0	0	0
KIT:55524161	0	0	0	0	0	0	0	0	0
KIT:55561658	0	0	0	0	0	0	0	0	0
KIT:55561805	0	0	0	0	0	0	0	0	0
KIT:55561861	0	0	0	0	0	0	0	0	0
KIT:55564614	0	0	0	0	0	0	0	0	0
KIT:55564616	0	0	0	0	0	0	0	0	0
KIT:55570043	0	0	0	0	0	0	0	0	0
KIT:55570067	0	0	0	0	0	0	0	0	0
KIT:55589871	0	0	0	0	0	0	0	0	0
KIT:55592059	0	0	0	0	0	0	0	0	0
KIT:55592061	0	0	0	0	0	0	0	0	0
KIT:55593551	0	0	0	0	0	0	0	0	0
KIT:55593560	0	0	0	0	0	0	0	0	0
KIT:55593608	0	0	0	0	0	0	0	0	0
KIT:55598029	0	0	0	0	0	0	0	0	0
KIT:55598065	0	0	0	0	0	0	0	0	0
...
</code>
</hidden>\\