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differential expression improvements (#452)

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* add cutoff for low expression genes in topN selection

* remove debugging printfs

* change cli param name for diffexp cutoff

* change CLI param name

* second try at diffexp - using lfc sort with pval cutoff

* use lfc cutoff

* update comments to match code; cap p-value adjustment to max of 1

* lint

* explain diffexp in readme

* add link

* add diffexp-lfc-cutoff to test config

* update test to match revised diffexp spec

* fix latent bug in GET arg handling that was breaking tests

* lint

* comment cleanup

* fix variance overestimation so it is symmetric

* lint
This commit is contained in:
Bruce Martin
2018-11-16 14:44:56 -08:00
committed by Charlotte Weaver
parent 3475f3f12e
commit 141f802824
8 changed files with 58 additions and 22 deletions
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docs/REST_API.md
+2 -2
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@@ -568,14 +568,14 @@ If differential expression is not supported by the server, must return an HTTP 5
**Response body:**
- For 200 Success, differential expression statistics returned as array of arrays sorted by varindex, where each contains the following values:
- For 200 Success, differential expression statistics returned as array of arrays, where each contains the following values:
- **varIndex**: variable index for the computed results
- **logfoldchange**: log fold-change of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first group,
- **pVal**: unadjusted p-value,
- **pValAdj**: adjusted p-value
Statistics are encoded as an array of arrays, with fields ordered as:
Values ordered as:
_varIndex_, _logfoldchange_, _pVal_, _pValAdj_