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authorFrederick Muriuki Muriithi2021-11-23 12:31:42 +0300
committerFrederick Muriuki Muriithi2021-11-23 12:31:42 +0300
commit845ab7696cdd7c7b2cdbd9b2b7f6b0a537d81117 (patch)
tree75b67351909970538101b58feeeaa12c88b6532f /gn3
parente1fb18b9d4a3b4ab9783f58d78ff384141567a42 (diff)
downloadgenenetwork3-845ab7696cdd7c7b2cdbd9b2b7f6b0a537d81117.tar.gz
Migrate `getPartialCorrelationsNormal`
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Migrate the `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsNormal` function in GN1. * Remove function obsoleted by newer implementation of the code
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/partial_correlations.py60
1 files changed, 44 insertions, 16 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 4f45159..4bd26a2 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -200,22 +200,6 @@ def good_dataset_samples_indexes(
samples_from_file.index(good) for good in
set(samples).intersection(set(samples_from_file))))
-def determine_partials(
- primary_vals, control_vals, all_target_trait_names,
- all_target_trait_values, method):
- """
- This **WILL** be a migration of
- `web.webqtl.correlation.correlationFunction.determinePartialsByR` function
- in GeneNetwork1.
-
- The function in GeneNetwork1 contains code written in R that is then used to
- compute the partial correlations.
- """
- ## This function is not implemented at this stage
- return tuple(
- primary_vals, control_vals, all_target_trait_names,
- all_target_trait_values, method)
-
def compute_partial_correlations_fast(# pylint: disable=[R0913, R0914]
samples, primary_vals, control_vals, database_filename,
fetched_correlations, method: str, correlation_type: str) -> Tuple[
@@ -330,3 +314,47 @@ def compute_partial(
return tuple(
__compute_trait_info__(target)
for target in zip(target_vals, target_names))
+
+def partial_correlations_normal(# pylint: disable=R0913
+ primary_vals, control_vals, input_trait_gene_id, trait_database,
+ data_start_pos: int, db_type: str, method: str) -> Tuple[
+ float, Tuple[float, ...]]:
+ """
+ Computes the correlation coefficients.
+
+ This is a migration of the
+ `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsNormal`
+ function in GeneNetwork1.
+ """
+ def __add_lit_and_tiss_corr__(item):
+ if method.lower() == "sgo literature correlation":
+ # if method is 'SGO Literature Correlation', `compute_partial`
+ # would give us LitCorr in the [1] position
+ return tuple(item) + trait_database[1]
+ if method.lower() in (
+ "tissue correlation, pearson's r",
+ "tissue correlation, spearman's rho"):
+ # if method is 'Tissue Correlation, *', `compute_partial` would give
+ # us Tissue Corr in the [1] position and Tissue Corr P Value in the
+ # [2] position
+ return tuple(item) + (trait_database[1], trait_database[2])
+ return item
+
+ target_trait_names, target_trait_vals = reduce(
+ lambda acc, item: (acc[0]+(item[0],), acc[1]+(item[data_start_pos:],)),
+ trait_database, (tuple(), tuple()))
+
+ all_correlations = compute_partial(
+ primary_vals, control_vals, target_trait_vals, target_trait_names,
+ method)
+
+ if (input_trait_gene_id and db_type == "ProbeSet" and method.lower() in (
+ "sgo literature correlation", "tissue correlation, pearson's r",
+ "tissue correlation, spearman's rho")):
+ return (
+ len(trait_database),
+ tuple(
+ __add_lit_and_tiss_corr__(item)
+ for idx, item in enumerate(all_correlations)))
+
+ return len(trait_database), all_correlations