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comparison rDiff/src/rdiff.m @ 0:0f80a5141704

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version 0.3 uploaded
author vipints
date Thu, 14 Feb 2013 23:38:36 -0500
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-1:000000000000 0:0f80a5141704
1 function []=rdiff(ARGS)
2 % rdiff()
3 %
4
5 if isempty(ARGS)
6 usage() ;
7 exit(-1) ;
8 end
9 %ARGS=[ARGS ':.:.'] ;
10
11 %%% Add paths %%%
12 fprintf('Set the paths\n')
13 CFG.paths = set_rdiff_paths();
14
15
16 %%% Read configuration file %%%
17 fprintf('Load configuration\n')
18 CFG = configure_rdiff(CFG);
19 CFG = process_command_line_args(CFG,ARGS);
20 CFG = process_configure_rdiff(CFG);
21
22 %%% Get read counts %%%
23
24 %load the gene structure
25 load(CFG.genes_path , 'genes');
26
27 % mask the regions which overlap with other genes
28 fprintf('Compute regions common to multiple genes\n')
29 [genes]=detect_overlapping_regions(genes);
30
31 %Precompute testing regions
32 fprintf('Compute alternative regions\n')
33 [genes]=compute_testing_region(CFG,genes);
34
35 %Get the gene expression
36 if CFG.estimate_gene_expression
37 fprintf('Measure gene expression\n')
38 get_read_counts(CFG,genes);
39 end
40
41 %%% Estimate variance function %%%
42 if CFG.perform_nonparametric
43 variance_function_nonparametric_1=[];
44 variance_function_nonparametric_2=[];
45 [variance_function_nonparametric_1, variance_function_nonparametric_2]=estimate_variance_nonparametric(CFG,genes);
46 end
47
48 if CFG.perform_poisson
49 variance_function_parametric_1=[];
50 variance_function_parametric_2=[];
51 end
52 if CFG.perform_parametric
53 variance_function_parametric_1=[];
54 variance_function_parametric_2=[];
55 [variance_function_parametric_1, variance_function_parametric_2]=estimate_variance_parametric(CFG,genes);
56 end
57
58 %If only gene expression is needed, stop here
59 if CFG.only_gene_expression
60 return
61 end
62
63
64 %%% Perform tests & Write output %%%
65
66 %Run the prametric tests
67 if or(CFG.perform_parametric,CFG.perform_poisson)
68 perform_parametric_tests(CFG,genes,variance_function_parametric_1, variance_function_parametric_2)
69 end
70 %Run the nonparametric tests
71 if or(CFG.perform_nonparametric,CFG.perform_mmd)
72 perform_nonparametric_tests(CFG,genes,variance_function_nonparametric_1, variance_function_nonparametric_2)
73 end
74
75 return
76
77
78