--bmr-modifier-file
The user can provide a BMR modifier for each gene in the ROI file, which is a multiplier for the categorized background mutation rates, before testing them against the gene's categorized mutation rates. Such a file can be used to correct for regional or systematic bias in mutation rates across the genome that may be correlated to CpG deamination or DNA repair processes like transcription-coupled repair or mismatch repair. Mutation rates have also been associated with DNA replication timing, where higher mutation rates are seen in late replicating regions. Note that the same per-gene multiplier is used on each mutation category of BMR. Any genes from the ROI file that are not in the BMR modifier file will be tested against unmodified overall BMRs per mutation category. BMR modifiers of <=0 are not permitted, because that's just silly.
--skip-low-mr-genes
Genes with consistently lower MRs than the BMRs across mutation categories, may show up in the results as an SMG (by CT or LRT). If such genes are not of interest, they may be assigned a p-value of 1. This should also speed things up. Genes with higher Indel or Truncation rates than the background will not be skipped even if the gene's overall MR is lower than the BMR. If bmr-modifiers are applied, this step uses the modified BMRs instead.

sub _doc_authors { return <<EOS Qunyuan Zhang, Ph.D. Cyriac Kandoth, Ph.D. Nathan D. Dees, Ph.D. EOS }

sub execute { my $self = shift; my $gene_mr_file = $self->gene_mr_file; my $output_file = $self->output_file; my $output_file_detailed = $output_file . "_detailed"; my $max_fdr = $self->max_fdr; my $skip_low_mr_genes = $self->skip_low_mr_genes; my $bmr_modifier_file = $self->bmr_modifier_file; my $processors = $self->processors;

    # Check on all the input data before starting work
    print STDERR "Gene mutation rate file not found or is empty: $gene_mr_file\n" unless( -s $gene_mr_file );
    print STDERR "BMR modifier file not found or is empty: $bmr_modifier_file\n" unless( !defined $bmr_modifier_file || -s $bmr_modifier_file );
    return undef unless( -s $gene_mr_file && ( !defined $bmr_modifier_file || -s $bmr_modifier_file ));

    # If BMR modifiers were provided, then load them, and create another gene_mr_file with modified BMRs
    if( defined $bmr_modifier_file ) {
        my $inBmrModFh = IO::File->new( $bmr_modifier_file ) or die "Couldn't open $bmr_modifier_file. $!\n";
        my %bmr_modifier = ();
        while( my $line = $inBmrModFh->getline ) {
            next if( $line =~ m/^#/ );
            chomp( $line );
            my ( $gene, $modifier ) = split( /\t/, $line );
            ( $modifier > 0 ) or die "$modifier is an invalid bmr-modifier. Please fix values in $bmr_modifier_file.\n";
            $bmr_modifier{$gene} = $modifier;
        }
        $inBmrModFh->close;

        my $new_gene_mr_file = Genome::Sys->create_temp_file_path;
        ( $new_gene_mr_file ) or die "Couldn't create a temp file. $!";
        my $inMrFh = IO::File->new( $gene_mr_file ) or die "Couldn't open $gene_mr_file. $!\n";
        my $outMrFh = IO::File->new( $new_gene_mr_file, ">" ) or die "Couldn't open $new_gene_mr_file. $!\n";
        while( my $line = $inMrFh->getline ) {
            if( $line =~ m/^#/ ) {
                $outMrFh->print( $line );
                next;
            }
            chomp( $line );
            my ( $gene, $type, $covd_bps, $mut_cnt, $bmr ) = split( /\t/, $line );
            $bmr = $bmr * $bmr_modifier{$gene} if( defined $bmr_modifier{$gene} );
            $outMrFh->print( "$gene\t$type\t$covd_bps\t$mut_cnt\t$bmr\n" );
        }
        $outMrFh->close;
        $inMrFh->close;

        $gene_mr_file = $new_gene_mr_file;
    }

    # Collect per-gene mutation rates for reporting in results later
    my ( %gene_muts, %gene_bps, %mut_classes_hash );
    my $inMrFh = IO::File->new( $gene_mr_file ) or die "Couldn't open $gene_mr_file. $!\n";
    while( my $line = $inMrFh->getline ) {
        next if( $line =~ m/^#/ );
        my ( $gene, $type, $covd_bps, $mut_cnt, undef ) = split( /\t/, $line );

        # Warn user about cases where there could be fewer covered bps than mutations detected
        ( $mut_cnt <= $covd_bps ) or warn "More $type seen in $gene than there are bps with sufficient coverage!\n";

        if( $type eq "Overall" or $type eq "Indels" or $type eq "Truncations" ) {
            $gene_muts{$gene}{$type} = $mut_cnt;
            $gene_bps{$gene} = $covd_bps;
            $mut_classes_hash{$type} = 1 unless( $type eq "Overall" );
        }
        elsif( $type =~ m/(Transitions|Transversions)$/ ) {
            $gene_muts{$gene}{SNVs} += $mut_cnt;
            $mut_classes_hash{SNVs} = 1;
        }
        else {
            die "Unrecognized mutation class in gene-mr-file. $!\n";
        }
    }
    $inMrFh->close;
    my @mut_classes = sort keys %mut_classes_hash;

    # Create a temporary intermediate file to hold the p-values
    my $pval_file = Genome::Sys->create_temp_file_path;
    ( $pval_file ) or die "Couldn't create a temp file. $!";

    # Call R for Fisher combined test, Likelihood ratio test, and convolution test on each gene
    my $smg_cmd = "R --slave --args < " . __FILE__ . ".R $gene_mr_file $pval_file smg_test $processors $skip_low_mr_genes";
    WIFEXITED( system $smg_cmd ) or croak "Couldn't run: $smg_cmd ($?)";

    # Call R for calculating FDR on the p-values calculated in the SMG test
    my $fdr_cmd = "R --slave --args < " . __FILE__ . ".R $pval_file $output_file_detailed calc_fdr $processors $skip_low_mr_genes";
    WIFEXITED( system $fdr_cmd ) or croak "Couldn't run: $fdr_cmd ($?)";

    # Parse the R output to identify the SMGs (significant by at least 2 of 3 tests)
    my $smgFh = IO::File->new( $output_file_detailed ) or die "Couldn't open $output_file_detailed. $!\n";
    my ( @newLines, @smgLines );
    my $header = "#Gene\t" . join( "\t", @mut_classes );
    $header .= "\tTot Muts\tCovd Bps\tMuts pMbp\tP-value FCPT\tP-value LRT\tP-value CT\tFDR FCPT\tFDR LRT\tFDR CT\n";
    while( my $line = $smgFh->getline ) {
        chomp( $line );
        if( $line =~ m/^Gene\tp.fisher\tp.lr\tp.convol\tfdr.fisher\tfdr.lr\tfdr.convol$/ ) {
            push( @newLines, $header );
            push( @smgLines, $header );
        }
        else {
            my ( $gene, @pq_vals ) = split( /\t/, $line );
            my ( $p_fcpt, $p_lrt, $p_ct, $q_fcpt, $q_lrt, $q_ct ) = @pq_vals;
            my @mut_cnts;
            foreach( @mut_classes ) {
                # If a mutation count is a fraction, round down the digits after the decimal point
                push( @mut_cnts, (( $gene_muts{$gene}{$_} =~ m/\./ ) ? sprintf( "%.2f", $gene_muts{$gene}{$_} ) : $gene_muts{$gene}{$_} ));
            }
            my $mut_per_mbp = ( $gene_bps{$gene} ? sprintf( "%.2f", ( $gene_muts{$gene}{Overall} / $gene_bps{$gene} * 1000000 )) : 0 );
            push( @newLines, join( "\t", $gene, @mut_cnts, $gene_muts{$gene}{Overall}, $gene_bps{$gene}, $mut_per_mbp, @pq_vals ) . "\n" );

            # If the FDR of at least two of these tests is less than the maximum allowed, we consider it an SMG
            if(( $q_fcpt <= $max_fdr && $q_lrt <= $max_fdr ) || ( $q_fcpt <= $max_fdr && $q_ct <= $max_fdr ) ||
               ( $q_lrt <= $max_fdr && $q_ct <= $max_fdr )) {
                push( @smgLines, join( "\t", $gene, @mut_cnts, $gene_muts{$gene}{Overall}, $gene_bps{$gene}, $mut_per_mbp, @pq_vals ) . "\n" );
            }
        }
    }
    $smgFh->close;

    # Add per-gene SNV and Indel counts to the detailed R output, and make the header friendlier
    my $outDetFh = IO::File->new( $output_file_detailed, ">" ) or die "Couldn't open $output_file_detailed. $!\n";
    $outDetFh->print( @newLines );
    $outDetFh->close;

    # Do the same for only the genes that we consider SMGs
    my $outFh = IO::File->new( $output_file, ">" ) or die "Couldn't open $output_file. $!\n";
    $outFh->print( @smgLines );
    $outFh->close;

    return 1;
}

1;

1 POD Error

The following errors were encountered while parsing the POD:

Around line 85:

=back doesn't take any parameters, but you said =back EOS ); }