R/get.mutation.frequencies.r

In IOstrovnaya/Clonality: Clonality testing

get.mutation.frequencies <-
function(xmut.ids, tcga.cancer.type=NULL, reference.data=NULL,combine.with.TCGA=FALSE ) {
  plus1<-TRUE
   if (! (all(substr(xmut.ids,1,1) %in% c(c(1:9),"X","Y") | substr(xmut.ids,1,2) %in% c(c(10:22)) )))
    stop("xmut.ids should be of the following format: {Chromosome Location RefAllele AltAllele}, each entry separated by space, \n where chromosome is a number 1-22 or X or Y; \n location is genomic location in  GRCh37 build; \n RefAllele is a reference allele and AltAllele is Alternative allele/Tumor_Seq_Allele2. \n For example '10 100003849 G A', is the mutation at chromosome 10, genomic location 100003849, where reference allele G is substituted with A, or \n '10 100011448 - CCGCTGCAAT' is the insertion of 'CCGCTGCAAT' at chromosome 10, location 100011448. \n The ref and alt alleles follow standard TCGA maf file notations.")

  if (is.null(tcga.cancer.type) & is.null(reference.data)) stop("You either need to specify 'tcga.cancer.type' to use TCGA based frequnecies or specify 'reference.data' to get reference dataset for frequency calculation")
  if (combine.with.TCGA & (is.null(tcga.cancer.type) | is.null(reference.data))) stop("If you choose combine.with.TCGA=TRUE, i.e. to combine reference dataset with TCGA data, then you  need to  specify both'tcga.cancer.type'  and 'reference.data' ")
  if (!combine.with.TCGA & (!is.null(tcga.cancer.type) & !is.null(reference.data))) warning("You choose combine.with.TCGA=FALSE, but specified both TCGA and reference data - only TCGA data will be used unless you choose combine.with.TCGA=TRUE")
  
  
  
  if (!is.null(reference.data)) #estimation using reference file
  { if (all(colnames(reference.data)!="Chromosome")) stop("reference.data should include column 'Chromosome' that will be used to create mutation IDs")
    if (all(colnames(reference.data)!="PatientID")) stop("reference.data should include column 'PatientID' - could be the same as sample IDs Tumor_Sample_Barcode")
    if (all(colnames(reference.data)!="Start_Position")) stop("reference.data should include column 'Start_Position' that will be used to create mutation IDs")
    if (all(colnames(reference.data)!="Reference_Allele")) stop("reference.data should include column 'Reference_Allele' that will be used to create mutation IDs")
    if (all(colnames(reference.data)!="Tumor_Seq_Allele2")) stop("reference.data should include column 'Tumor_Seq_Allele2' that will be used to create mutation IDs")
    if (all(colnames(reference.data)!="Tumor_Sample_Barcode")) stop("reference.data should include column 'Tumor_Sample_Barcode' that will be used in frequency calculation")
    
    reference.data$mut<-paste(reference.data$Chromosome,reference.data$Start_Position,reference.data$Reference_Allele,reference.data$Tumor_Seq_Allele2)
    if (any(duplicated(paste(reference.data$mut,reference.data$PatientID))))
    {
      reference.data<-reference.data[!duplicated(paste(reference.data$mut,reference.data$PatientID)),]
    }
    
    
    if (all(xmut.ids %in%  reference.data$mut) & all(reference.data$mut %in% xmut.ids )) 
    {#warning("All mutations in xmut.ids are observed in the reference dataset, and vice versa. See help file for more info. ")
      plus1<-FALSE
    }
    else
      
      n<-length(unique(reference.data$PatientID))  
    if (n<50 & is.null(tcga.cancer.type)) warning(paste("reference dataset has only",n,"patients - frequency estimation might be not very accurate")    )
    
    fref<-NULL
    for (i in xmut.ids) fref<-c(fref,length(unique(reference.data$PatientID[reference.data$mut==i])) )
    
    if (all(fref==0,na.rm=T))    warning("None of the mutations in 'xmut.ids' were seen in this reference dataset. Make sure  'xmut.ids' are in the correct format: check ?get.mutation.frequencies")
    if (  plus1==TRUE)
      freq<-(fref+1)/(n+1)
    else   freq<-fref/n
    
    
    
  }
  
  if (!is.null(tcga.cancer.type)) #estimation using TCGA
      { if ((tcga.cancer.type %in% c("COAD", "LUAD",  "BRCA"))) data(freqdata)
        if (!(tcga.cancer.type %in% colnames(freqdata))) 
    stop("This function relies on object 'freqdata' that contains frequencies from 3 tcga cancer types:  COAD, LUAD, and BRCA.\n 'tcga.cancer.type' has to be one of these 3 abbreviations.   \n Full set of 33 cancer types is available by loading a full object in GitHub 'load(url(\"https://github.com/IOstrovnaya/MutFreq/blob/master/freqdata.RData?raw=true\"))' that contains cancer types:  
ACC  BLCA BRCA CESC CHOL COAD DLBC ESCA GBM  HNSC KICH KIRC KIRP LAML LGG  LIHC LUAD LUSC MESO OV   PAAD PCPG PRAD READ SARC SKCM STAD TGCT THCA THYM UCEC UCS  UVM \n See https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations for details")
 f<-freqdata[match(xmut.ids,rownames(freqdata)), tcga.cancer.type]
  names(f)<-xmut.ids
  if (all(is.na(f)))    warning("None of the mutations were seen in TCGA.  Make sure  xmut.ids are in the correct format: check ?get.mutation.frequencies")
  if (all(f==0,na.rm=T))    warning("None of the mutations were seen in this TCGA subtype. Make sure  xmut.ids are in the correct format: check ?get.mutation.frequencies")
  f[is.na(f)]<-0
  
  
    freq<-(f+1)/(freqdata[1, tcga.cancer.type]+1)
    
  }
  
  
  
  if (combine.with.TCGA & !is.null(reference.data) & !is.null(tcga.cancer.type))
{     if (  plus1==TRUE) freq<-(fref+f+1)/(freqdata[1, tcga.cancer.type]+n+1)
  else freq<-(fref+f)/(freqdata[1, tcga.cancer.type]+n)
 
  
}  
  
  names(freq)<-xmut.ids
freq
}