Mercurial > repos > vipints > rdiff
comparison rDiff/src/tests/get_nonparametric_masks.m @ 0:0f80a5141704
version 0.3 uploaded
| author | vipints |
|---|---|
| date | Thu, 14 Feb 2013 23:38:36 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:0f80a5141704 |
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| 1 function [MASKS]=get_nonparametric_masks(CFG,reads1,reads2) | |
| 2 | |
| 3 %What fracitons should be choosen for the cutoff | |
| 4 cen_arr=0.1:0.1:1; | |
| 5 | |
| 6 % Define the mask which should be used in order to mask high | |
| 7 % expresse genes | |
| 8 MASKS=zeros(length(cen_arr),size(reads1,2)); | |
| 9 | |
| 10 COUNTER=1; | |
| 11 for censor_frac= cen_arr | |
| 12 temp_reads1=reads1; | |
| 13 temp_reads2=reads2; | |
| 14 %cut to relvant position | |
| 15 read_coverage=sum(reads1,1)+sum(reads2,1); | |
| 16 % get positions with a positive coverage | |
| 17 nonzero_position=read_coverage>0; | |
| 18 %Determine the cutoff values | |
| 19 sorted_coverage=sort(read_coverage(nonzero_position)); | |
| 20 nr_of_nonzero_positions=sum(nonzero_position); | |
| 21 relevant_positions=read_coverage<=sorted_coverage(ceil(nr_of_nonzero_positions*censor_frac)); | |
| 22 MASKS(COUNTER,relevant_positions)=1; | |
| 23 COUNTER=COUNTER+1; | |
| 24 end |