NAME

MyBioinfo::Common - Commonly used Perl subroutines for my bioinformatics work.

SYNOPSIS

  use MyBioinfo::Common;
  or
  use MyBioinfo::Common qw(mean_r mad padjBH raw_sum2 raw_sum_mean raw_sum_var MchooseN BH_fdr raw_sum_dir raw_sum nb_pval_v2 nb_pval raw_mean_dir raw_mean nb_stat var fold_change chi_stat readnamelist readnamewithinfolist array2hash max min sum mean median log2 log10 read_norm2 rescale_cutoff read_cutoff isAboveCutoff rescale_norm_max rescale_norm_sum1 is_all_zero fprecision unique)

  my $s = &nb_stat($ref_q, $q_size, $start_pos, $num_rep, $epsilon, $step, $cur_pos);
  my $fc = &fold_change($treatment_val, $control_val);
  my $s = &chi_stat($obs, $n, $prob);
  &readnamelist($filename, \@array);
  &readnamewithinfolist($filename, \@hash);
  &array2hash(\@ref_array, \@ref_hash);
  my $m = &max(@array);
  my $m = &min(@array);
  my $s = &sum(@array);
  my $m = &mean(@array);
  my $m = &median(@array);
  my $v = &log2($m);
  &read_norm2($filename, \@treatment, \@control);
  &rescale_norm_max(\@normalization, $max_norm);
  &rescale_norm_sum1(\@normalization, $sum_norm);
  my $boolean = &is_all_zero(\@array);
  my @formatted = &fprecision($n_after_decimal, @array);
  &read_cutoff($filename, \@treatment, \@control);

DESCRIPTION

  Some convenient functions for my bioinformatics work. 

EXPORT

  fold_change
  chi_stat
  readnamelist
  readnamewithinfolist
  array2hash
  max
  min
  sum
  mean
  median
  log2
  read_norm2
  rescale_norm_max
  rescale_norm_sum1
  is_all_zero
  fprecision

SEE ALSO

MyBioinfo::Math

MyBioinfo::NBTest

AUTHOR

Li Shen, <shenli.sam@gmail.com>

COPYRIGHT AND LICENSE

Copyright (C) 2010-2013 by Li Shen

diffReps goes under GNU GPL v3: http://www.gnu.org/licenses/gpl.html