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comparison rDiff/src/variance/estimate_variance_parametric.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 [VARIANCE1, VARIANCE2]=estimate_variance_parametric(CFG,genes)
2
3 fprintf('Estimating variance function for rDiff.parametric\n')
4
5 VARIANCE1=[];
6 VARIANCE2=[];
7
8 %Get the gene expression
9 fprintf('Loading gene expression\n')
10 if isempty(CFG.Counts_gene_expression)
11 EXPR_TAB_FILENAME=[CFG.out_base 'Gene_expression.tab'];
12 else
13 EXPR_TAB_FILENAME=CFG.Counts_gene_expression;
14 end
15
16 try
17 Gene_expression=importdata(EXPR_TAB_FILENAME,'\t',1);
18 catch
19 error(['Could not open: ' EXPR_TAB_FILENAME])
20 end
21 %C=importdata('../out/release_test/Gene_expression.tab','\t',1);
22
23
24 %Get the counts
25 fprintf('Loading alternative region counts\n')
26 if isempty(CFG.Counts_rDiff_parametric)
27 IN_FILENAME=[CFG.out_base 'Alternative_region_counts.mat'];
28 load(IN_FILENAME,'Counts_rDiff_parametric')
29 else
30 IN_FILENAME=[CFG.out_base CFG.Counts_rDiff_parametric];
31 load(IN_FILENAMEc,'Counts_rDiff_parametric')
32 end
33
34 %Iterate over the functions to be generated
35 %compute means and variances
36
37 if CFG.compute_variance_function_1
38 fprintf('estimating variance function for sample 1\n')
39 %Get the samples to use for the for estimation the variance function
40 if CFG.merge_sample1
41 SAMPLE_IX=find(CFG.SAMPLES);
42 else
43 SAMPLE_IX=find(CFG.SAMPLES==1);
44 end
45 VARIANCE1=estimate_variance_helper(CFG,SAMPLE_IX,Counts_rDiff_parametric,Gene_expression.data);
46 if not(isempty(CFG.save_variance_function_1))
47 VARIANCE_FUNTION_OUTPATH=[CFG.out_base CFG.save_variance_function_1];
48 save(VARIANCE_FUNTION_OUTPATH,'VARIANCE1');
49 else
50 %Use previously estimated variance function
51 if not(isempty(CFG.variance_function_1))
52 try
53 VARIANCE_FUNTION_INPATH=[CFG.out_base CFG.variance_function_1];
54 VARIANCE1=load(VARIANCE_FUNTION_INPATH);
55 catch
56 error(['Could not load variance function for sample 1 from: ' VARIANCE_FUNTION_INPATH])
57 end
58 end
59 end
60 end
61
62 if CFG.compute_variance_function_2
63 fprintf('estimating variance function for sample 2\n')
64 %Get the samples to use for the for estimation the variance function
65 if CFG.merge_sample2
66 SAMPLE_IX=find(CFG.SAMPLES);
67 else
68 SAMPLE_IX=find(CFG.SAMPLES==2);
69 end
70 VARIANCE2=estimate_variance_helper(CFG,SAMPLE_IX,Counts_rDiff_parametric,Gene_expression.data);
71 if not(isempty(CFG.save_variance_function_2))
72 VARIANCE_FUNTION_OUTPATH=[CFG.out_base CFG.save_variance_function_2];
73 save(VARIANCE_FUNTION_OUTPATH,'VARIANCE2');
74 else
75 %Use previously estimated variance function
76 if not(isempty(CFG.variance_function_2))
77 try
78 VARIANCE_FUNTION_INPATH=[CFG.out_base CFG.variance_function_2];
79 VARIANCE2=load(VARIANCE_FUNTION_INPATH);
80 catch
81 error(['Could not load variance function for sample 2 from: ' VARIANCE_FUNTION_INPATH])
82 end
83 end
84 end
85 end
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