Mercurial > repos > vipints > deseq_hts

annotate deseq-hts_2.0/src/mask_dubl.m @ 10:2fe512c7bfdf draft

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DESeq2 version 1.0.19 added to the repo
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 08:15:34 -0400
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2fe512c7bfdf DESeq2 version 1.0.19 added to the repo
vipints <vipin@cbio.mskcc.org>
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1 function [new_genes]=mask_dubl(genes,THRESH);
2fe512c7bfdf DESeq2 version 1.0.19 added to the repo
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2
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3 CHROMOSOMES={};
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4 COUNTER=1;
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5 for i=1:size(genes,2)
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6 CHROMOSOMES{COUNTER}=genes(i).chr;
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7 COUNTER=COUNTER+1;
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8 end
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9 CHROMOSOMES=unique(CHROMOSOMES);
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10
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11
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12 INFO=zeros(size(genes,2),4);
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13 for i=1:size(genes,2)
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14 CHR_VAL=0;
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15 for chr= 1:length(CHROMOSOMES)
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16 if strcmp(genes(i).chr,CHROMOSOMES(chr))
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17 CHR_VAL=chr;
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18 end
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19 end
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20 INFO(i,:)=[i,genes(i).start,genes(i).stop, CHR_VAL];
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21 end
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22
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23 COUNTER=1;
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24 new_genes=genes;
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25 for chr= 1:length(CHROMOSOMES)
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26 GENES_ON_CHR=INFO(INFO(:,4)==chr,:);
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27 [TEMP,POS]=sort(GENES_ON_CHR(:,2));
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28 GENES_ON_CHR=GENES_ON_CHR(POS,:);
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29 STARTS=GENES_ON_CHR(:,2);
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30 STOPS=GENES_ON_CHR(:,3);
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31 for i=1:(size(GENES_ON_CHR,1))
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32 MIN_START=find(STOPS>=STARTS(i),1,'first');
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33 MAX_STOP=find(STARTS<=STOPS(i),1,'last');
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34 if MIN_START==i
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35 MIN_START=[];
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36 end
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37 if MAX_STOP==i
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38 MAX_STOP=[];
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39 end
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40 EXONS=[];
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41 if not (isempty(MIN_START))
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42 for CURR=MIN_START:(i-1)
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43 if(not(isempty(genes(GENES_ON_CHR(CURR,1)).transcripts)))
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44 for tra=1:size(genes(GENES_ON_CHR(CURR,1)).transcripts,2)
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45 if(not(isempty(genes(GENES_ON_CHR(CURR,1)).exons)))
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46 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).exons{tra}];
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47 else
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48 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).start,genes(GENES_ON_CHR(CURR,1)).stop];
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49 end
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50 end
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51 else
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52 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).start,genes(GENES_ON_CHR(CURR,1)).stop];
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53 end
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54 end
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55 end
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56 if not (isempty(MAX_STOP))
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57 for CURR=(i+1):MAX_STOP
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58 if(not(isempty(genes(GENES_ON_CHR(CURR,1)).transcripts)))
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59 for tra=1:size(genes(GENES_ON_CHR(CURR,1)).transcripts,2)
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60 if(not(isempty(genes(GENES_ON_CHR(CURR,1)).exons)))
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61 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).exons{tra}];
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62 else
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63 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).start,genes(GENES_ON_CHR(CURR,1)).stop];
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64 end
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65 end
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66 else
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67 EXONS=[EXONS;genes(GENES_ON_CHR(CURR,1)).start,genes(GENES_ON_CHR(CURR,1)).stop];
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68 end
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69
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70 end
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71 end
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72 if not (isempty([MAX_STOP,MIN_START]))
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73 EXONS=EXONS(EXONS(:,2)>=STARTS(i),:);
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74 EXONS=EXONS(EXONS(:,1)<=STOPS(i),:);
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75 new_genes(GENES_ON_CHR(i,1)).non_unique_regions=EXONS;
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76 else
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77 new_genes(GENES_ON_CHR(i,1)).non_unique_regions=[];
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78 end
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79 end
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80 COUNTER=COUNTER+1;
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81 end