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Annotation of copy-number-regulated genes #10

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raylim opened this issue May 8, 2015 · 5 comments
Closed

Annotation of copy-number-regulated genes #10

raylim opened this issue May 8, 2015 · 5 comments

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@raylim
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raylim commented May 8, 2015

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raylim referenced this issue Jun 24, 2015
@inodb
Fixes 16 Add gene annotations
c5ee717 
Adds Kandoth, Lawrence and Cancer Gene Census annotations to the vcf files.
Changes hap_insuf postfix rule to one gene_ann postfix rule that adds all
annotations at once.
@raylim raylim closed this as completed Jun 24, 2015
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inodb commented Jun 24, 2015

Actually that commit added gene annotations but not the copy number regulated genes annotations

@inodb inodb reopened this Jun 24, 2015
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inodb commented Jun 24, 2015

That still needs to be done. Problem was that it can add a lot of columns, since the annotation is per subtype so we need some way of choosing what annotations to add. Maybe as a parameter to the Makefile

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raylim commented Jun 25, 2015

how sparse is the matrix per subtype? Maybe we could collapse it into a single annotation column

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raylim commented Jun 25, 2015

i.e., a single column that lists the number of subtypes where a gene is copy-number regulated

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inodb commented Jun 25, 2015

I guess that could work as well

@inodb inodb closed this as completed in 8e68dc4 Jul 21, 2015
inodb added a commit that referenced this issue Jul 21, 2015
@inodb
Merge pull request #25 from inodb/add_cn_reg_annotations
cc09a03 
Fix #10 Add copy number regulated annotation
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