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> setwd("C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass")
> library("SplicingCompass2.1")
> packageDescription("SplicingCompass2.1")
Package: SplicingCompass2.1
Type: Package
Title: What the package does (short line)
Version: 1.0
Date: 2015-10-22
Author: Who wrote it
Maintainer: Who to complain to <yourfault@somewhere.net>
Description: More about what it does (maybe more than one line)
License: What license is it under?
Depends: methods
Collate: 01_calculateJunctionDimensionsCore.R experimentInfoCore.R countTableCore.R gffParser.r myImagePlot_.R .....
Packaged: 2015-10-22 14:53:26 UTC; skanter
Built: R 3.3.2; ; 2017-04-11 13:27:47 UTC; windows

-- File: C:/Users/Aniko/Documents/R/win-library/3.3/SplicingCompass2.1/Meta/package.rds 
> expInf=new("ExperimentInfo")
> expInf=setDescription(expInf,"ControlVsO18")
> expInf=setGroupInfo(expInf,
+                     groupName1="control",sampleNumsGroup1=1:4,
+                     groupName2="O18",sampleNumsGroup2=5:8)
> covBedCountFilesControl=c(
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_1.gff",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_2.gff",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_3.gff",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_4.gff")
> covBedCountFilesO18=c(
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_5.gff",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_6.gff",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_7.gff",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_8.gff")
> expInf=setCovBedCountFiles(expInf,c(covBedCountFilesControl,covBedCountFilesO18))
> junctionBedFilesControl=c(
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_1.bed",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_2.bed",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_3.bed",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_4.bed")
> junctionBedFilesO18=c(
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_5.bed",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_6.bed",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_7.bed",
+   "C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_8.bed")
> expInf=setJunctionBedFiles(expInf,c(junctionBedFilesControl,junctionBedFilesO18))
> expInf=setReferenceAnnotation(expInf,"hf38mergedTranscript.gtf")
> referenceAnnotationFormat=list(IDFieldName="geneSymbol",idValSep=" ")
> expInf=setReferenceAnnotationFormat(expInf,referenceAnnotationFormat)
> checkExperimentInfo(expInf)
Read CovBedCountFile: 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_1.gff 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_2.gff 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_3.gff 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_4.gff 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_5.gff 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_6.gff 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_7.gff 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/bed_counted_hit_hf38/covBedCountedHits_sample_8.gff 
Read JunctionBedFiles: 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_1.bed 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_2.bed 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_3.bed 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_4.bed 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_5.bed 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_6.bed 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_7.bed 
C:/Users/Aniko/Dropbox/Munka/PhD/results/abroad_semester/R/SplicingCompass/SJ_bed_in_use/junctionsBed_sample_8.bed 
Read reference annotation...Done.

ExperimentInfo: Only lines with the following chromosome names will be used for the calculations:

 chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr2 chr20 chr21 chr22 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrM chrX chrY 

Unused chromosome names are:

 chr1_gl000191_random chr1_gl000192_random chr1_KI270706v1_random chr1_KI270711v1_random chr1_KI270712v1_random chr1_KI270713v1_random chr1_KI270714v1_random chr1_KI270760v1_alt chr1_KI270766v1_alt chr10chr10_GL383545v1_alt chr10chr10_GL383546v1_alt chr10chr10_KI270824v1_alt chr10chr10_KI270825v1_alt chr11_JH159136v1_alt chr11_JH159137v1_alt chr11_KI270721v1_random chr11_KI270831v1_alt chr11_KI270832v1_alt chr11_KI270903v1_alt chr11_KI270903v1_altchr11chr11_KI270830v1_alt chr11chr11_KI270826v1_alt chr11chr11_KI270827v1_alt chr11chr11_KI270829v1_alt chr11chr11_KI270832v1_alt chr11chr11_KI270927v1_alt chr12_GL383552v1_alt chr12_GL877876v1_alt chr12_KI270904v1_alt chr12chr12_GL383550v2_alt chr12chr12_GL383551v1_alt chr12chr12_GL877875v1_alt chr12chr12_GL877876v1_altchr12_KI270904v1_alt chr12chr12_KI270833v1_alt chr12chr12_KI270835v1_alt chr13chr13_KI270838v1_alt chr13chr13_KI270842v1_alt chr14_GL000009v2_random chr14_GL000194v1_random chr14_KI270726v1_random chr14_KI270846v1_alt chr14_KI2... <truncated>

Check input chromosome names for consistency.

Number of input files ok?
[1] TRUE
> countTable=new("CountTable")
> countTable=setExperimentInfo(countTable,expInf)
> countTable=constructCountTable(countTable,nCores=1,printDotPerGene=TRUE)
Processing CoverageBed output files:
  |===============                                                                                                          |  12%
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  scan() expected 'a real', got 'D00614:183:CABNAANXX:3:1107:7896:66038'
> 