R/sigpro.R

In mishugeb/SigProR: Extracts Mutational Signatures from Cancer Genomes and Decompose the Signatures into Global Signatures

#' sigprofilerextractor
#' @description Extracts De Novo signature from genomes and Decomposes the De Novo Signatures to Cosmic Signatures
#'
#' @param input_type input_type: A string. Type of input. The type of input should be one of the following:\cr
#' ----- "vcf": used for vcf format inputs.\cr
#' ----- "table": used for table format inputs using a tab seperated file.\cr

#' @param output A string. The name of the output folder. The output folder will be generated in the current working directory.\cr
#' @param inputdata A string. Name of the input folder (in case of "vcf" type input) or the input file (in case of "table"  type input).\cr
#' The project file or folder should be inside the current working directory.\cr
#' For the "vcf" type input,the project has to be a folder which will contain the vcf files in vcf format or text formats.\cr
#' The "text"type projects have to be a file.
#' @param refgen A string, optional. The name of the reference genome. The default reference genome is "GRCh37". This parameter is applicable only if the input_type is "vcf".\cr
#' @param genome_build
#' @param minsigs A positive integer, optional. The minimum number of signatures to be extracted. The default value is 1
#' @param maxsigs A positive integer, optional. The maximum number of signatures to be extracted. The default value is 10
#' @param replicates A positive integer, optional. The number of iteration to be performed to extract each number signature. The default value is 8
#' @param mtype A  strings, optional. The items in the list defines the mutational contexts to be considered to extract the signatures. The default value is "96,DINUCS,ID",\cr
#'  where "96" is the SBS96 context, "DINUC" is the DINULEOTIDE context and ID is INDEL context. Each context should be written in a single string separated by "," without any space.
#' @param init A string. Represents the NMF initialization. Options are "random", "nndsvdar" and "nndsvd"
#' @param exome Boolean, optional. Defines if the exomes will be extracted. The default value is "False".
#' @param cpu An integer, optional. The number of processors to be used to extract the signatures. The default value is -1 which will use all available processors.
#'
#' @return a folder with results
#' @export sigprofilerextractor
#'
#' @examples
sigprofilerextractor <- function(input_type, output, inputdata, refgen = 'GRCh37', genome_build="GRCh37",minsigs = 1, maxsigs = 3,  replicates=5, mtype = c('96,DINUCS,ID'), init="random",exome=F, cpu=-1) {

  sys <- reticulate::import("sys")
  sigpro <- reticulate::import("sigproextractor.sigpro")


  minsigs=as.integer(minsigs)
  maxsigs = as.integer(maxsigs)
  replicates=as.integer(replicates)
  exome=FALSE
  cpu = as.integer(cpu)
  sigpro$sigProfilerExtractor(input_type, output, inputdata, refgen = 'GRCh38',genome_build="GRCh38",startProcess=minsigs, endProcess = maxsigs, totalIterations=replicates, exome=exome, init=init)
  sys$stdout$flush()

}



#' Title
#'
#' @param datatype The type of example data. There are two types: 1."table", 2."vcf"
#'
#' @return The path of the explample data
#' @export importdata
#'
#' @examples
importdata <- function(datatype){
  sigpro <- reticulate::import("sigproextractor.sigpro")
  project = sigpro$importdata(datatype)
  return(project)
}



#' decomposition
#' @description Decomposes the De Novo Signatures to Cosmic Signatures
#' @param signatures A string. Path to a  tab delimited file that contains the signaure table where the rows are mutation types and colunms are signature IDs.
#' @param activities A string. Path to a tab delimilted file that contains the activity table where the rows are sample IDs and colunms are signature IDs.
#' @param samples  A string. Path to a tab delimilted file that contains the activity table where the rows are mutation types and colunms are sample IDs.
#' @param output A string. Path to the output folder.
#' @param mutation_type A string. The context type. Example: "96", "192", "1536", "6144", "INDEL", "DINUC". The default value is "96".
#' @param genome_build A string. The genome type. Example: "GRCh37", "GRCh38", "mm9", "mm10". The default value is "GRCh37"
#' @param verbose Boolean. Prints statements. Default value is False.
#'
#' @return A folder with decomposition results The files below will be generated in the output folder: \cr
#'    \cr
#'    1.comparison_with_global_ID_signatures.csv \cr
#     2.Decomposed_Solution_Activities.txt \cr
#'    3.Decomposed_Solution_Samples_stats.txt \cr
#'    4.Decomposed_Solution_Signatures.txt \cr
#'    5.decomposition_logfile.txt \cr
#'    6.Mutation_Probabilities.txt \cr
#'    7.Signature_assaignment_logfile.txt \cr
#'    8.Signature_plot[MutatutionContext]_plots_Decomposed_Solution.pdf
#' @export decomposition
#'
#' @examples
decomposition <- function(signatures, activities, samples, output, mutation_type="96", genome_build="GRCh37", verbose=F){
  decompose <-reticulate::import("sigproextractor.decomposition")
  result = decomposition$decompose(signatures, activities, samples, output, mutation_type="96", genome_build="GRCh37", verbose=False)
  return(result)
}

#' Title
#'
#' @param genome
#' @param custom
#' @param rsync
#' @param bash
#' @param ftp
#'
#' @return
#' @export install
#'
#' @examples
install <- function(genome, custom=F, rsync=F, bash=T, ftp=T){
  os <- reticulate::import("os")
  sys <- reticulate::import("sys")
  genInstall <- reticulate::import("SigProfilerMatrixGenerator.install")
  genInstall$install(genome, custom, rsync, bash, ftp)
  sys$stdout$flush()
}