data-raw/build_sox2Examples.R

In chedonat/OncoPhase: SOMATIC MUTATION CELLULAR PREVALENCE COMPUTATION

#library(OncoPhase.R)

#Chromosomes
##########
#Chromsomes list
chrom_list<-paste("chr",c(1:22,"X","Y","M"),sep="")
#Chromosomes sizes
hg19_dfsize<-list(chr1=249250621,chr2=243199373,chr3=198022430, chr4=191154276, chr5=180915260, chr6=171115067,
                   chr7=159138663, chr8=146364022, chr9=141213431, chr10=135534747, chr11=135006516, chr12=133851895,
                   chr13=115169878, chr14=107349540,chr15=102531392, chr16=90354753, chr17=81195210, chr18=78077248,
                   chr19=59128983, chr20=63025520,chr21=48129895,chr22=51304566, chrX=155270560, chrY=59373566,chrM=16571)


build_sox2Data<-function(Patient, chrom){



  data_directory =  paste("../../OCCA/",Patient,"/",sep="")

  samples_information_df<-read.csv(paste(data_directory,"samples_",Patient,".csv",sep=""),header=T)
 # sample_list<- initsSamples(samples_information_df)



  cat("\n\n Load the Phasing Association")
  file_phase=paste(data_directory,
                   "Phasing/phasingassociation_somatic_germline_1_", Patient,".paf",sep="")
  phasingassociation_df<- read.table( file = file_phase,header=T,row.names=1, sep="\t")
  phasingassociation_df <- phasingassociation_df[phasingassociation_df$Chrom==chrom,]



  cat("\n\n Load the master snp wellcount")
  filesnpwellcount<-paste(data_directory,"Master/Chromosomes/AllelesCount_mastermatrix_",Patient,"_",chrom,".tsv.bz2",sep="")
  mastersnpwellcountmatrix_df<- read.table( file = filesnpwellcount,header=T,row.names=1,sep="\t")


  cat("\n\n Load the master ref wellcount")
  filerefwellcount<-paste(data_directory,"Master/Chromosomes/RefAllelesCount_mastermatrix_",Patient,"_",chrom,".tsv.bz2",sep="")
  masterrefwellcountmatrix_df<- read.table( file = filerefwellcount,header=T,row.names=1,sep="\t")

  # cat("\n\n Load the master well fraction")
  # file_wellfraction<-paste(data_directory,"Master/Chromosomes/AllelesFraction_mastermatrix_",Patient,"_",chrom,".tsv.bz2",sep="")
  # masterwellfractionmatrix_df<- read.table( file = file_wellfraction,header=T,row.names=1,sep="\t")
  #



  #Keeping only the tumour samples with LFR wells data
  tumoursamples= as.character(samples_information_df[samples_information_df$alleletype=="LFR_wells","name"])

  columns_list=c("Chrom","Start","End","Vartype","Ref","All","IsGermline", tumoursamples)

  mastersnpwellcountmatrix_df=mastersnpwellcountmatrix_df[columns_list]
  masterrefwellcountmatrix_df=masterrefwellcountmatrix_df[columns_list]





  cat("\n\n Load the copynumbers")

  #CopyNumber_df = data.frame()
  MajorCopyNumber_df=data.frame()
  MinorCopyNumber_df= data.frame()
  CNVFraction_df= data.frame()

  copynumber_groups = unique(as.character(samples_information_df[samples_information_df$alleletype=="LFR_wells","cnvprofile"]))
  print(copynumber_groups)
  for(cngroup in copynumber_groups)
  {
    filecngroup<-  paste(data_directory,"CopyNumber/cn_",cngroup,"_",chrom,".csv",sep="")
    if (!file.exists(filecngroup))
    {
      cat("\n\n\t The file ",filecngroup, " do not exists" )
      next
    }


    newcopynumber<- read.csv( file = filecngroup,header=T,row.names=1)
    #We need to change the rownames so that to be only the chromosome and the position.// We remove this point of the code in the next versions.
    #make.unique since for sure we should have the same copy numbe rprofile at a particular position of the genome
    rownames(newcopynumber) = make.unique(unlist(lapply(rownames(newcopynumber), function(x) paste(strsplit(x,"_")[[1]][1:2],collapse="_"))))


    if(ncol(MajorCopyNumber_df)==0)
    {
      # CopyNumber_df=newcopynumber[,"CopyNumber",drop=F]
      MajorCopyNumber_df=newcopynumber[,"MajorCopyNumber",drop=F]
      MinorCopyNumber_df=newcopynumber[,"MinorCopyNumber",drop=F]
      CNVFraction_df=1-newcopynumber[,"NormalFraction",drop=F]
    }else
    {
      # CopyNumber_df=cbind(CopyNumber_df,newcopynumber[,"CopyNumber",drop=F])
      MajorCopyNumber_df=cbind(MajorCopyNumber_df, newcopynumber[,"MajorCopyNumber",drop=F])
      MinorCopyNumber_df=cbind(MinorCopyNumber_df, newcopynumber[,"MinorCopyNumber",drop=F])
      CNVFraction_df=cbind(CNVFraction_df,1-newcopynumber[,"NormalFraction",drop=F])
    }
  }
  #names(CopyNumber_df) = copynumber_groups
  names(MajorCopyNumber_df) = copynumber_groups
  names(MinorCopyNumber_df) = copynumber_groups
  names(CNVFraction_df) = copynumber_groups


  # Expanding the copy number matrices

  Major_cn_sample_G_df=as.data.frame(matrix(ncol=length(tumoursamples),nrow=nrow(MajorCopyNumber_df)))
  colnames(Major_cn_sample_G_df) = tumoursamples
  rownames(Major_cn_sample_G_df) = rownames(MajorCopyNumber_df)
  CNVFraction_cn_sample_G_df= Major_cn_sample_G_df
  Minor_cn_sample_G_df= Major_cn_sample_G_df

  #We fill the matrice with the apropriate copy number
  for(sample in tumoursamples)
  {
    cnv_profile= as.character(samples_information_df[samples_information_df$name==sample,"cnvprofile"])
    CNVFraction_cn_sample_G_df[sample]=CNVFraction_df[cnv_profile]
    Major_cn_sample_G_df[sample]=MajorCopyNumber_df[cnv_profile]
    Minor_cn_sample_G_df[sample]=MinorCopyNumber_df[cnv_profile]
  }



  # Uniformizing the list of mutations, The allelecounts and the copynumbe rtables shouls have the same list of mutations.

  masterrefwellcountmatrix_df["chrom_pos"]=paste(masterrefwellcountmatrix_df$Chrom,masterrefwellcountmatrix_df$End,sep="_")
 # masterrefwellcountmatrix_df["rownames"] = rownames(masterrefwellcountmatrix_df)


  chrom_pos_alleleinfo=as.character(unlist(masterrefwellcountmatrix_df["chrom_pos"]))
  chrom_pos_copynumber = rownames(Major_cn_sample_G_df)
  chrom_pos_intersect=intersect(chrom_pos_alleleinfo, chrom_pos_copynumber)

  rownames(masterrefwellcountmatrix_df) = make.unique(chrom_pos_alleleinfo)
  rownames(mastersnpwellcountmatrix_df) = make.unique(chrom_pos_alleleinfo)


  Major_cn_sample_G_df=Major_cn_sample_G_df[chrom_pos_intersect,]
  Minor_cn_sample_G_df=Minor_cn_sample_G_df[chrom_pos_intersect,]
  CNVFraction_cn_sample_G_df=  CNVFraction_cn_sample_G_df[chrom_pos_intersect,]
  masterrefwellcountmatrix_df=masterrefwellcountmatrix_df[chrom_pos_intersect,]
  mastersnpwellcountmatrix_df=mastersnpwellcountmatrix_df[chrom_pos_intersect,]

  rownames(masterrefwellcountmatrix_df) = paste(masterrefwellcountmatrix_df$Chrom,masterrefwellcountmatrix_df$End,masterrefwellcountmatrix_df$Ref,masterrefwellcountmatrix_df$All,sep="_")
  rownames(mastersnpwellcountmatrix_df) = rownames(masterrefwellcountmatrix_df)
  rownames(Major_cn_sample_G_df) = rownames(masterrefwellcountmatrix_df)
  rownames(Minor_cn_sample_G_df) = rownames(masterrefwellcountmatrix_df)
  rownames(CNVFraction_cn_sample_G_df) = rownames(masterrefwellcountmatrix_df)

  mastersnpwellcountmatrix_df["chrom_pos"] = NULL
  masterrefwellcountmatrix_df["chrom_pos"] = NULL

  phasing_association_df=phasingassociation_df
 # phasing_association_df=phasingassociation_df["Phased_List"]
 # names(phasing_association_df) = "Phased_List"



  snp_allelecount_df=mastersnpwellcountmatrix_df
  ref_allelecount_df=masterrefwellcountmatrix_df
  major_copynumber_df = Major_cn_sample_G_df
  minor_copynumber_df = Minor_cn_sample_G_df
  CNVFraction_df = CNVFraction_cn_sample_G_df
  nbFirstColumns=6
  region = chrom


  dataset=list(snp_allelecount_df=snp_allelecount_df, ref_allelecount_df=ref_allelecount_df,
               phasing_association_df=phasing_association_df, major_copynumber_df=major_copynumber_df,
               minor_copynumber_df=minor_copynumber_df,CNVFraction_df=CNVFraction_df,
               tumoursamples=tumoursamples)



  dataset


}







cat("\n\n\n Chromosome 10\n\n")

chr10_XYZ101 = build_sox2Data("11152","chr10")
devtools::use_data(chr10_XYZ101,overwrite=T)
#cs=chr10_11152
####masterprevalence_df=getPrevalenceMultiSamples(cs$snp_allelecount_df, cs$ref_allelecount_df, cs$major_copynumber_df,cs$minor_copynumber_df, phasing_association_df = cs$phasing_association_df,cnv_fraction=cs$CNVFraction_df  ,nbFirstColumns=6, tumoursamples=cs$tumoursamples )


stop()


cat("\n Header \n\n")
####print(head(masterprevalence_df))



cat("\n\n\n Chromosome 15\n\n")

chr15_11152 = build_sox2Data("11152","chr15")
devtools::use_data(chr15_11152,overwrite=T)
cs=chr15_11152
####masterprevalence_df=getPrevalenceMultiSamples(cs$snp_allelecount_df, cs$ref_allelecount_df, cs$major_copynumber_df,cs$minor_copynumber_df, phasing_association_df = cs$phasing_association_df,cnv_fraction=cs$CNVFraction_df  ,nbFirstColumns=6, tumoursamples=cs$tumoursamples )

cat("\n Header \n\n")
####print(head(masterprevalence_df))






cat("\n\n\n Chromosome 18\n\n")

chr18_11152 = build_sox2Data("11152","chr18")
devtools::use_data(chr18_11152,overwrite=T)
cs=chr18_11152
####masterprevalence_df=getPrevalenceMultiSamples(cs$snp_allelecount_df, cs$ref_allelecount_df, cs$major_copynumber_df,cs$minor_copynumber_df, phasing_association_df = cs$phasing_association_df,cnv_fraction=cs$CNVFraction_df  ,nbFirstColumns=6, tumoursamples=cs$tumoursamples )

cat("\n Header \n\n")
####print(head(masterprevalence_df))






cat("\n\n\n Chromosome 22\n\n")

chr22_11152 = build_sox2Data("11152","chr22")
devtools::use_data(chr22_11152,overwrite=T)
cs=chr22_11152
####masterprevalence_df=getPrevalenceMultiSamples(cs$snp_allelecount_df, cs$ref_allelecount_df, cs$major_copynumber_df,cs$minor_copynumber_df, phasing_association_df = cs$phasing_association_df,cnv_fraction=cs$CNVFraction_df  ,nbFirstColumns=6, tumoursamples=cs$tumoursamples )

cat("\n Header \n\n")
####print(head(masterprevalence_df))






#Take the sample list from a csv files, can also be entered manually