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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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server/app/rest_api/rest.py
+2 -2
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@@ -346,7 +346,7 @@ class DataObsAPI(Resource):
def get(self):
accept_type = request.args.get("accept-type", None)
# request.args is immutable
args = dict(request.args)
args = request.args.copy()
args.pop("accept-type", None)
try:
filter_ = parse_filter(ImmutableMultiDict(args), current_app.data.schema['annotations'])
@@ -450,7 +450,7 @@ class DataVarAPI(Resource):
def get(self):
accept_type = request.args.get("accept-type", None)
# request.args is immutable
args = dict(request.args)
args = request.args.copy()
args.pop("accept-type", None)
try:
filter_ = parse_filter(ImmutableMultiDict(args), current_app.data.schema['annotations'])