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> # Analysis script for the Yeast GeneExpression
> # Paper senior author: RBrem 20??, Published in: Plos
> #
> # (C) 2012 Danny Arends - GBIC - University of Groningen
> #   - Files are distributed with the Rctl package in Rctl/tests
> 
> # Start by: 
> # setwd("~/Github/Rpackages/CTLmapping/Rctl/tests")
> 
> library(ctl)
Loading required package: MASS
Loading required package: parallel
Loading required package: qtl
> 
> probeannot <- read.csv("GeneExpression_Yeast_Annotation.txt", sep="\t", header=TRUE, row.names=1)
> cross <- read.cross("csvr", file="GeneExpression_Yeast_RBrem.csvr", geno=c("AA","AB"))
 --Read the following data:
	 109  individuals
	 282  markers
	 301  phenotypes
 --Cross type: bc 
> cross <- convert2riself(cross)
> cross <- fill.geno(cross)                   # Fill the genotypes
> cross <- calc.genoprob(cross)               # Calculate genotype probabilities
> 
> ctls  <- CTLscan.cross(cross, phenocol = c(1:5), qtl = FALSE, verbose = TRUE)
Data 301 phenotypes, 109/109 individuals, 282 markers
Data checks finished after: 0 seconds
Data ranking finished after: 0.01 seconds
R_mapctl, verbose=1Phenotype 1: Mapping, toLOD
Phenotype A_06_P1085: Done after 0.14 0 seconds
R_mapctl, verbose=1Phenotype 2: Mapping, toLOD
Phenotype A_06_P6147: Done after 0.13 0 seconds
R_mapctl, verbose=1Phenotype 3: Mapping, toLOD
Phenotype A_06_P3469: Done after 0.14 0 seconds
R_mapctl, verbose=1Phenotype 4: Mapping, toLOD
Phenotype A_06_P4255: Done after 0.14 0 seconds
R_mapctl, verbose=1Phenotype 5: Mapping, toLOD
Phenotype A_06_P2638: Done after 0.12 0 seconds
Done after: 0.68 seconds
> 
> for(x in 1:5) {
+   qtls <- scanone(cross, pheno.col = x)     # Scan for QTLS
+   ctls[[x]]$qtls <- qtls[,3]
+ }
Warning message:
In checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,  :
  Dropping 4 individuals with missing phenotypes.

> map   <- qtls[,1:2]                         # Get the genetic map
> 
> nodes <- ctl.lineplot(ctls, map, significance = 0.1) # Line plot all the phenotypes
p_above= 0 
p_above= 0 
p_above= 0 
p_above= 0 
p_above= 0 
p_above= 0 
p_above= 1 
p_above= 1 
p_above= 0 
p_above= 0 
Found 4 significant CTLs
Warning: Phenotype 50 from 4 no CTL/QTL information
Warning: Phenotype 50 from 4 no CTL/QTL information
Warning: Phenotype 50 from 4 no CTL/QTL information
Warning: Phenotype 50 from 4 no CTL/QTL information
Direction of CTL unknown, NA detected: 933.5 21 933.5 
Direction of CTL unknown, NA detected: 933.5 21 933.5 
Direction of CTL unknown, NA detected: 933.5 22 933.5 
Direction of CTL unknown, NA detected: 933.5 22 933.5 
> nodes
     TRAIT1 MARKER TRAIT2    LOD_C CAUSAL LOD_T1 LOD_T2
[1,]      4     12     50 1.687753     NA      0     NA
[2,]      4     13     50 1.687753     NA      0     NA
[3,]      4     14     50 1.687753     NA      0     NA
[4,]      4     15     50 1.687753     NA      0     NA
> 
> 
> proc.time()
   user  system elapsed 
   1.28    0.09    1.35