options.default

Description

A function to return default options in sARTP and rARTP. This page is for illustration. Users do not need to call this function explicitly.

Usage

options.default()

Value

A list of options.

See Also

options

Examples

options <- options.default()
str(options)
names(options)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ARTP2)
Loading required package: Formula
Loading required package: data.table
Loading required package: parallel
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ARTP2/options.default.Rd_%03d_medium.png", width=480, height=480)
> ### Name: options.default
> ### Title: options.default
> ### Aliases: options.default
> 
> ### ** Examples
> 
> options <- options.default()
> str(options)
List of 40
 $ out.dir             : chr "/home/ddbj/DataUpdator-rgm3/target"
 $ id.str              : chr "PID"
 $ method              : num 3
 $ nperm               : num 1e+05
 $ snp.miss.rate       : num 0.05
 $ maf                 : num 0.05
 $ HWE.p               : num 1e-05
 $ chr.R2              : num 0.95
 $ gene.R2             : num 0.95
 $ gene.miss.rate      : num 1
 $ group.gap           : NULL
 $ rm.gene.subset      : logi TRUE
 $ turn.off.filters    : logi FALSE
 $ delete              : logi TRUE
 $ print               : logi TRUE
 $ tidy                : logi TRUE
 $ save.setup          : logi TRUE
 $ path.setup          : NULL
 $ only.setup          : logi FALSE
 $ keep.geno           : logi FALSE
 $ seed                : num 1
 $ nthread             : int 4
 $ excluded.snps       : NULL
 $ selected.snps       : NULL
 $ excluded.regions    : NULL
 $ excluded.subs       : NULL
 $ selected.subs       : NULL
 $ excluded.genes      : NULL
 $ meta                : logi FALSE
 $ only.meta           : logi TRUE
 $ inspect.snp.n       : num 5
 $ inspect.snp.percent : num 0
 $ inspect.gene.n      : num 10
 $ inspect.gene.percent: num 0.05
 $ trim.huge.chr       : logi TRUE
 $ huge.gene.size      : num 1000
 $ huge.chr.size       : num 2000
 $ huge.gene.R2        : num 0.85
 $ huge.chr.R2         : num 0.85
 $ version             :Classes 'package_version', 'numeric_version'  hidden list of 1
  ..$ : int [1:3] 0 9 22
> names(options)
 [1] "out.dir"              "id.str"               "method"              
 [4] "nperm"                "snp.miss.rate"        "maf"                 
 [7] "HWE.p"                "chr.R2"               "gene.R2"             
[10] "gene.miss.rate"       "group.gap"            "rm.gene.subset"      
[13] "turn.off.filters"     "delete"               "print"               
[16] "tidy"                 "save.setup"           "path.setup"          
[19] "only.setup"           "keep.geno"            "seed"                
[22] "nthread"              "excluded.snps"        "selected.snps"       
[25] "excluded.regions"     "excluded.subs"        "selected.subs"       
[28] "excluded.genes"       "meta"                 "only.meta"           
[31] "inspect.snp.n"        "inspect.snp.percent"  "inspect.gene.n"      
[34] "inspect.gene.percent" "trim.huge.chr"        "huge.gene.size"      
[37] "huge.chr.size"        "huge.gene.R2"         "huge.chr.R2"         
[40] "version"             
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>