Bio-ViennaNGS
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# types are typedef'ed and only the typedef is referenced, never the tag name.# The default value is: NO.TYPEDEF_HIDES_STRUCT = NO# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This# cache is used to resolve symbols given their name and scope. Since this can be# an expensive process and often the same symbol appears multiple times in the# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small# doxygen will become slower. If the cache is too large, memory is wasted. The# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536# symbols. At the end of a run doxygen will report the cache usage and suggest# 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# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open links to# external symbols imported via tag files in a separate window.# The default value is: NO.# This tag requires that the tag GENERATE_HTML is set to YES.EXT_LINKS_IN_WINDOW = NO# Use this tag to change the font size of LaTeX formulas included as images in# the HTML documentation. When you change the font size after a successful# doxygen run you need to manually remove any form_*.png images from the HTML# output directory to force them to be regenerated.# Minimum value: 8, maximum value: 50, default value: 10.# This tag requires that the tag GENERATE_HTML is set to YES.FORMULA_FONTSIZE = 10# Use the FORMULA_TRANPARENT tag to determine whether or not the images# generated for formulas are transparent PNGs. Transparent PNGs are not# 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# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see# http://www.mathjax.org) which uses client side Javascript for the rendering# instead of using prerendered bitmaps. Use this if you do not have LaTeX# installed or if you want to formulas look prettier in the HTML output. When# enabled you may also need to install MathJax separately and configure the path# to it using the MATHJAX_RELPATH option.# The default value is: NO.# This tag requires that the tag GENERATE_HTML is set to YES.USE_MATHJAX = NO# When MathJax is enabled you can set the default output format to be used for# the MathJax output. See the MathJax site (see:# http://docs.mathjax.org/en/latest/output.html) for more details.
# it.# The default directory is: latex.# This tag requires that the tag GENERATE_LATEX is set to YES.LATEX_OUTPUT = latex# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be# invoked.## Note that when enabling USE_PDFLATEX this option is only used for generating# bitmaps for formulas in the HTML output, but not in the Makefile that is# written to the output directory.# The default file is: latex.# This tag requires that the tag GENERATE_LATEX is set to YES.LATEX_CMD_NAME = latex# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate# index for LaTeX.# The default file is: makeindex.# This tag requires that the tag GENERATE_LATEX is set to YES.
# the PDF file directly from the LaTeX files. Set this option to YES to get a# higher quality PDF documentation.# The default value is: YES.# This tag requires that the tag GENERATE_LATEX is set to YES.USE_PDFLATEX = YES# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode# command to the generated LaTeX files. This will instruct LaTeX to keep running# if errors occur, instead of asking the user for help. This option is also used# when generating formulas in HTML.# The default value is: NO.# This tag requires that the tag GENERATE_LATEX is set to YES.LATEX_BATCHMODE = NO# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the# index chapters (such as File Index, Compound Index, etc.) in the output.# The default value is: NO.# This tag requires that the tag GENERATE_LATEX is set to YES.
lib/Bio/ViennaNGS/Expression.pm view on Meta::CPAN
sortbed($bedname_u,"./",$bedname,1,undef);# sort bed file}subcomputeTPM {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/$length;}# 2. for computng actual TPM valuesforeach$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;}subcomputeRPKMfromTPM {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 readsforeach$i(keys%{${$self->data}[$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 0.640 second using v1.01-cache-2.11-cpan-5f2e87ce722 )