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> ## Purpose: Test script for pedgene package
> ## Testing a simple 10-variant gene on both the X chrom and autosome
> ## Authors: Dan Schaid and Jason Sinnwell
> ## Created: 19-AUG-2013
> ## Updated: 9/8/2025
> 
> devel=FALSE
> if(devel) {
+   .libPaths(c("/projects/bsi/pharmacogenetics/s212953.SchaidMethods/PedGene/Build/gitbranch/renv/library/R-4.4/x86_64-pc-linux-gnu/",.libPaths()))
+   library(CompQuadForm)
+   library(Pedixplorer)
+   library(survey)
+   dir="../"
+   rfiles <- list.files("../R/", pattern="*.R", full=TRUE)
+   for(rf in rfiles) source(rf)
+   dfiles <- list.files(path=paste0(dir,"/data/"), pattern="*.RData$")
+   for(d in dfiles) load(paste0(dir, "/data/",d))
+ 
+ } else {
+   ## alternatively:
+   
+   require(pedgene)
+ 
+   data(example.ped)
+   data(example.geno)
+   data(example.map)
+ }
Loading required package: pedgene
Loading required package: Matrix
Loading required package: CompQuadForm
Loading required package: survey
Loading required package: grid
Loading required package: survival

Attaching package: 'survey'

The following object is masked from 'package:graphics':

    dotchart

Loading required package: Pedixplorer
> 
> 
> 
> ## simple tests of two genes (10 variants each)
> ## the genes are same variants, just on chroms 1 and X
> pg.m2 <- pedgene(example.ped, example.geno, example.map, male.dose=2)
> 
> pg.m1 <- pedgene(example.ped, example.geno, example.map, male.dose=1)
> 
> 
> ## saved objects are of class pedgene, with items call (function call)
> ## and pgdf, a data.frame with a row for each gene
> class(pg.m2)
[1] "pedgene"
> names(pg.m2)
[1] "pgdf" "call" "save"
> 
> 
> print(pg.m2, digits=4)
  gene chrom n.variant n.noninform stat.kernel pval.kernel stat.burden
1   AA     1         7           3       144.8      0.3498      -2.048
2   AX     X         7           3       124.1      0.2038      -2.168
  pval.burden
1     0.04061
2     0.03019
> 
> 
> print(pg.m1, digits=4)
  gene chrom n.variant n.noninform stat.kernel pval.kernel stat.burden
1   AA     1         7           3      144.83      0.3498      -2.048
2   AX     X         7           3       31.01      0.3297      -1.776
  pval.burden
1     0.04061
2     0.07578
> 
> summary(pg.m2)

Summary for pedgene object: 

Call:
pedgene(ped = example.ped, geno = example.geno, map = example.map, 
    male.dose = 2)


  gene chrom n.variant n.noninform stat.kernel pval.kernel stat.burden
1   AA     1         7           3    144.8264   0.3498380   -2.047518
2   AX     X         7           3    124.0772   0.2037578   -2.167566
  pval.burden
1  0.04060727
2  0.03019169
> 
> ## Testing first gene with dose=2-dose
> geno.recode <- cbind(example.geno[,1:2], 2-example.geno[,grep("AA", names(example.geno))])
> pg.recode <- pedgene(example.ped, geno.recode, male.dose=2)
> 
> ## note when map not given, assumes all 1 gene, and assigns "unknown" gene/chrom
> pg.recode
     gene   chrom n.variant n.noninform  stat.kernel pval.kernel stat.burden
1 unknown unknown         7           3 2.472408e-49   0.9986723 0.001904113
  pval.burden
1   0.9984807
> 
> proc.time()
   user  system elapsed 
   5.31    0.32    5.64