Mercurial > repos > dongjun > mosaics
view mosaics/R/base_reportSummary.R @ 2:b6d0c6ceda2c draft
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author | dongjun |
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date | Thu, 10 Jan 2013 15:56:15 -0500 |
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.reportSummary <- function( summaryFile, resultList, chipFile=NULL, chipFileFormat=NULL, controlFile=NULL, controlFileFormat=NULL, binfileDir=NULL, peakFile=NULL, peakFileFormat=NULL, byChr=FALSE, FDR=0.05, fragLen=200, binSize=fragLen, capping=0, analysisType="IO", d=0.25, signalModel="BIC", maxgap=fragLen, minsize=50, thres=10 ) { cat( "MOSAiCS: Summary of model fitting and peak calling\n", file=summaryFile ) cat( "\n", file=summaryFile, append=TRUE ) cat( "------------------------------------------------------------\n", file=summaryFile, append=TRUE ) cat( "Input/output file settings\n", file=summaryFile, append=TRUE ) cat( "------------------------------------------------------------\n", file=summaryFile, append=TRUE ) cat( "\n", file=summaryFile, append=TRUE ) cat( "Name of aligned read file (ChIP): ",chipFile,"\n", sep="", file=summaryFile, append=TRUE ) cat( "Aligned read file format (ChIP):", chipFileFormat, "\n", file=summaryFile, append=TRUE ) cat( "\n", file=summaryFile, append=TRUE ) cat( "Name of aligned read file (control): ",controlFile,"\n", sep="", file=summaryFile, append=TRUE ) cat( "Aligned read file format (control):", controlFileFormat, "\n", file=summaryFile, append=TRUE ) cat( "\n", file=summaryFile, append=TRUE ) for ( ff in 1:length(peakFileFormat) ) { cat( "Name of peak result file: ",peakFile[ff],"\n", sep="", file=summaryFile, append=TRUE ) cat( "Peak result file format:", peakFileFormat[ff], "\n", file=summaryFile, append=TRUE ) cat( "\n", file=summaryFile, append=TRUE ) } #cat( "\n", file=summaryFile, append=TRUE ) cat( "------------------------------------------------------------\n", file=summaryFile, append=TRUE ) cat( "Parameter settings\n", file=summaryFile, append=TRUE ) cat( "------------------------------------------------------------\n", file=summaryFile, append=TRUE ) cat( "\n", file=summaryFile, append=TRUE ) if ( byChr ) { cat( "Genome-wide or chromosome-wise analysis? Chromosome-wise analysis\n", file=summaryFile, append=TRUE ) } else { cat( "Genome-wide or chromosome-wise analysis? Genome-wide analysis\n", file=summaryFile, append=TRUE ) } if ( analysisType=="OS" ) { analysisTypeOut <- "One-sample analysis" } else if ( analysisType=="TS" ) { analysisTypeOut <- "Two-sample analysis (with mappability & GC content)" } else if ( analysisType=="IO" ) { analysisTypeOut <- "Two-sample analysis (Input only)" } if ( signalModel=="BIC" ) { signalModelOut <- "Automatic signal model selection based on BIC" } else if ( signalModel=="1S" ) { signalModelOut <- "One-signal-component model" } else if ( signalModel=="2S" ) { signalModelOut <- "Two-signal-component model" } cat( "False discovery rate (FDR):", FDR, "\n", file=summaryFile, append=TRUE ) cat( "Fragment length:", fragLen, "\n", file=summaryFile, append=TRUE ) cat( "Bin size:", binSize, "\n", file=summaryFile, append=TRUE ) if ( capping > 0 ) { cat( "Maximum number of reads allowed in each nucleotide:", capping, "\n", file=summaryFile, append=TRUE ) } cat( "Analysis type:", analysisTypeOut, "\n", file=summaryFile, append=TRUE ) cat( "d:", d, "\n", file=summaryFile, append=TRUE ) cat( "Signal model:", signalModelOut, "\n", file=summaryFile, append=TRUE ) cat( "maxgap:", maxgap, "\n", file=summaryFile, append=TRUE ) cat( "minsize:", minsize, "\n", file=summaryFile, append=TRUE ) cat( "thres:", thres, "\n", file=summaryFile, append=TRUE ) cat( "\n", file=summaryFile, append=TRUE ) cat( "------------------------------------------------------------\n", file=summaryFile, append=TRUE ) cat( "Peak calling summary\n", file=summaryFile, append=TRUE ) cat( "------------------------------------------------------------\n", file=summaryFile, append=TRUE ) cat( "\n", file=summaryFile, append=TRUE ) outFormat <- data.frame( resultList$chrID, resultList$n_peaks, resultList$peak_width, resultList$opt_sig_model, stringsAsFactors=FALSE ) colnames(outFormat) <- c( "chrID", "# peaks", "Median peak width", "Optimal/specified signal model" ) cat( as.character(colnames(outFormat)), file=summaryFile, sep="\t", append=TRUE ) cat( "\n", file=summaryFile, append=TRUE ) cat( rep("-----",3), file=summaryFile, sep="\t", append=TRUE ) cat( "\t\t\t-----", file=summaryFile, sep="\t", append=TRUE ) cat( "\n", file=summaryFile, append=TRUE ) # peak list for ( i in 1:nrow(outFormat) ) { cat( as.character(outFormat[i,])[1:3], file=summaryFile, sep="\t", append=TRUE ) cat( "\t\t", as.character(outFormat[i,])[4], file=summaryFile, sep="\t", append=TRUE ) cat( "\n", file=summaryFile, append=TRUE ) } }