User Tools

Trace:

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

— write [2016/04/13 18:02] (current)
Line 1: Line 1:
 +===== 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>​\\

Page Tools

SEQPower

Site Tools