Mercurial > repos > vipints > deseq_hts
diff deseq-hts_2.0/src/remove_reads_from_other_genes.m @ 10:2fe512c7bfdf draft
DESeq2 version 1.0.19 added to the repo
author | vipints <vipin@cbio.mskcc.org> |
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date | Tue, 08 Oct 2013 08:15:34 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq-hts_2.0/src/remove_reads_from_other_genes.m Tue Oct 08 08:15:34 2013 -0400 @@ -0,0 +1,21 @@ +function [READS_OUT,FLAG]=remove_reads_from_other_genes(READS,GENE) +%This funtion removes the reads in READS which could ome from other +%annotated genes. FLAG is 1 if this was sucsesfull and 0 otherwise +READS_IN=READS; +if isfield(GENE,'non_unique_regions') + EXONS=GENE.non_unique_regions; + IDX=zeros(1,GENE.stop-GENE.start+1); + + for i=1:size(EXONS,1) + START=max(EXONS(i,1),GENE.start)-GENE.start+1; + STOP=min(EXONS(i,2),GENE.stop)-GENE.start+1; + IDX(START:STOP)=1; + end + READS=READS(not(sum(READS(:,IDX>0),2)==sum(READS,2)),:); + FLAG=1; + READS_OUT=READS; +else + READS_OUT=READS_IN; + FLAG=0; +end +