Bio-ViennaNGS
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# types are typedef'ed and only the typedef is referenced, never the tag name.
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TYPEDEF_HIDES_STRUCT = NO
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# the optimal cache size from a speed point of view.
# Minimum value: 0, maximum value: 9, default value: 0.
LOOKUP_CACHE_SIZE = 0
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
TREEVIEW_WIDTH = 250
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EXT_LINKS_IN_WINDOW = NO
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FORMULA_FONTSIZE = 10
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# supported properly for IE 6.0, but are supported on all modern browsers.
#
# Note that when changing this option you need to delete any form_*.png files in
# the HTML output directory before the changes have effect.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_TRANSPARENT = YES
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USE_MATHJAX = NO
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LATEX_BATCHMODE = NO
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lib/Bio/ViennaNGS/Expression.pm view on Meta::CPAN
sortbed($bedname_u,"./",$bedname,1,undef); # sort bed file
}
sub computeTPM {
my ($self,$sample,$rl) = @_;
my ($TPM,$T,$totalTPM) = (0)x3;
my ($i,$meanTPM);
# iterate through $self->data[$i] twice:
# 1. for computing T (denominator in TPM formula)
foreach $i (keys %{${$self->data}[$sample]}){
my $count = ${${$self->data}[$sample]}{$i}{count};
my $length = ${${$self->data}[$sample]}{$i}{length};
#print "count: $count\nlength: $length\n";
$T += $count * $rl / $length;
}
# 2. for computng actual TPM values
foreach $i (keys %{${$self->data}[$sample]}){
my $count = ${${$self->data}[$sample]}{$i}{count};
lib/Bio/ViennaNGS/Expression.pm view on Meta::CPAN
$meanRPKM = $totalRPKM/$self->nr_features;
return $meanRPKM;
}
sub computeRPKMfromTPM {
my ($self,$sample,$rl) = @_;
my ($R,$T,$length,$count,$totalRPKM) = (0)x5;
my ($i,$meanRPKM);
# iterate through $self->data[$i] twice:
# 1. compute T (denominator in TPM formula) and total number of reads
foreach $i (keys %{${$self->data}[$sample]}){
$count = ${${$self->data}[$sample]}{$i}{count};
$length = ${${$self->data}[$sample]}{$i}{length};
#print "count: $count\nlength: $length\n";
$T += $count * $rl / $length;
$R += $count;
}
# print "T: $T\tR: $R\n";
# 2. compute RPKM from TPM
( run in 0.630 second using v1.01-cache-2.11-cpan-3cd7ad12f66 )