lohspec 12/19

DESCRIPTION

@@ -47,6 +47,8 @@ Collate:
     'VEP_Virtual-class.R'
     'VEP-class.R'
     'VEP_v88-class.R'
+    'VarScanFormat_Virtual-class.R'
+    'VarScanFormat-class.R'
     'Waterfall-class.R'
     'cnFreq.R'
     'cnFreq_buildMain.R'
@@ -95,6 +97,8 @@ Collate:
     'ideoView_buildMain.R'
     'ideoView_formatCytobands.R'
     'ideoView_qual.R'
+    'lohSpec-class.R'
+    'lohSpec-methods.R'
     'lohSpec.R'
     'lohSpec_buildMain.R'
     'lohSpec_fileGlob.R'

NAMESPACE

@@ -6,6 +6,7 @@ export(MutSpectra)
 export(MutationAnnotationFormat)
 export(TvTi)
 export(VEP)
+export(VarScanFormat)
 export(Waterfall)
 export(cnFreq)
 export(cnSpec)
@@ -24,17 +25,23 @@ exportClasses(GMS)
 exportClasses(MutSpectra)
 exportClasses(MutationAnnotationFormat)
 exportClasses(VEP)
+exportClasses(VarScanFormat)
 exportClasses(Waterfall)
+exportClasses(lohSpec)
 exportMethods(drawPlot)
+exportMethods(getChrBoundaries)
 exportMethods(getData)
 exportMethods(getDescription)
 exportMethods(getGrob)
 exportMethods(getHeader)
+exportMethods(getLohData)
+exportMethods(getLohSlidingWindow)
 exportMethods(getMeta)
 exportMethods(getMutation)
 exportMethods(getPath)
 exportMethods(getPosition)
 exportMethods(getSample)
+exportMethods(getVarScan)
 exportMethods(getVersion)
 exportMethods(writeData)
 import(data.table)

R/AllGenerics.R

@@ -535,7 +535,6 @@ setGeneric(
 #' @rdname lohSpec_qual-methods
 #' @param object Object of class VarScanFormat
 #' @param ... additional arguments to passed
-#' @exportMethod lohSpec_qual
 setGeneric(
     name="lohSpec_qual",
     def=function(object, ...){standardGeneric("lohSpec_qual")}

R/MutationAnnotationFormat-class.R

@@ -35,7 +35,6 @@ setClass("MutationAnnotationFormat",
 #' @importFrom data.table fread
 #' @export
 MutationAnnotationFormat <- function(path, version="auto", verbose=FALSE){
-    browser()
     mafData <- suppressWarnings(data.table::fread(input=path,
                                                   stringsAsFactors=TRUE,
                                                   verbose=verbose))

R/VarScanFormat-class.R

@@ -42,6 +42,17 @@ setClass("VarScanFormat",
                       http://varscan.sourceforge.net/somatic-calling.html#somatic-output
                       for appropriate columns and column names.")
              }
+
+             ## Check to see if the VAF columns are percentages as opposed to proportions
+             tumor_false <- any(grepl("%", object@varscan$tumor_var_freq) == FALSE)
+             normal_false <- any(grepl("%", object@varscan$normal_var_freq) == FALSE)
+             if (tumor_false == TRUE | normal_false == TRUE) {
+                 stop("Make sure the tumor/normal VAF column is in percentages and not proportion. 
+                      (i.e. 75.00% as opposed to 0.75)")
+             }
+
+             ## Check to see if the VAF provided are somatic or not
+
              return(TRUE)
          }
 )
@@ -64,6 +75,7 @@ VarScanFormat <- function(path, verbose=FALSE) {
     varscanData$sample <- "HCC1395"
     ## Get the sample names
     sample <- varscanData[,which(colnames(varscanData)=="sample"), with=FALSE]
+    length(colnames(varscanData))
 
     ## Create the varscan object
     varscanObject <- new(Class="VarScanFormat", path=path, varscan=varscanData, sample=sample)

R/VarScanFormat_Virtual-class.R

@@ -10,6 +10,7 @@
 #' @slot sample data.table object holding sample data.
 #' @importClassesFrom data.table data.table
 #' @import methods
+#' 
 setClass(
     Class="VarScanFormat_Virtual",
     representation=representation(varscan="data.table",

R/lohSpec-class.R

@@ -14,10 +14,6 @@
 #' @exportClass lohSpec
 #' @importFrom data.table data.table
 #' @importFrom gtable gtable
-#' @importFrom GenVisR multi_cytobandRet
-#' @importFrom GenVisR multi_chrBound
-#' @importFrom GenVisR cytoGeno
-#' @import methods
 methods::setOldClass("gtable")
 setClass(
     Class="lohSpec",
@@ -55,9 +51,7 @@ setClass(
 #' normal variant allele frequency to be used in Loss of Heterozygosity 
 #' calculations. defaults to .50\%
 
-path <- "~/Google Drive/varscan.example.tsv"
-varscanObject <- VarScanFormat(path = path)
-input <- varscanObject
+
 lohSpec <- function(input, chr=NULL, samples=NULL, y=NULL, genome='hg19',
                     gender=NULL, step=1000000, window_size=2500000, 
                     normal=.50, gradient_midpoint=.2, gradient_low="#ffffff",
@@ -98,11 +92,17 @@ setClass("lohData",
 lohData <- function(object, chr, samples, y, genome, step, window_size, 
                     normal, verbose) {
     ## Get the primary loh data
+    object <- VarScanFormat(path = "~/Google Drive/HCC1395.varscan.tsv")
     primaryData <- getLohData(object=object, chr=chr, verbose = verbose)
 
     ## Quality check on the primary data
+    ## To-Do: Put the quality check in the validity check
     primaryData <- lohSpec_qual(object=primaryData)
 
+    library(BiocInstaller)
+    biocLite("BSgenome.Hsapiens.UCSC.hg19")
+    BSgenome <- getBSgenome(genome = "BSgenome.Hsapiens.UCSC.hg19")
+
     ## Get the chromosome data
     if(is.null(y)) {
         y <- data.table()