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fix: adding data specific p-value filters #788

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merged 9 commits into from
Sep 30, 2024
Merged

fix: adding data specific p-value filters #788

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73b97a3
fix: adding data specific fillters
addramir Sep 24, 2024
0077370
Merge branch 'dev' into yt_adding_data_specific_fillters
addramir Sep 24, 2024
0f5b669
Merge branch 'dev' into yt_adding_data_specific_fillters
addramir Sep 25, 2024
f629e63
Merge branch 'dev' into yt_adding_data_specific_fillters
addramir Sep 25, 2024
9d66127
fix: removing variables
addramir Sep 25, 2024
88e4dd6
Merge branch 'dev' into yt_adding_data_specific_fillters
DSuveges Sep 26, 2024
996fe3a
Merge branch 'dev' into yt_adding_data_specific_fillters
addramir Sep 30, 2024
5c57ab4
fix: adding options to init
addramir Sep 30, 2024
3b95cfd
Merge branch 'dev' into yt_adding_data_specific_fillters
DSuveges Sep 30, 2024
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8 changes: 7 additions & 1 deletion src/gentropy/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -122,10 +122,16 @@ class GWASCatalogSumstatsPreprocessConfig(StepConfig):
class EqtlCatalogueConfig(StepConfig):
"""eQTL Catalogue step configuration."""

session: Any = field(
default_factory=lambda: {
"start_hail": True,
}
)
eqtl_catalogue_paths_imported: str = MISSING
eqtl_catalogue_study_index_out: str = MISSING
eqtl_catalogue_credible_sets_out: str = MISSING
mqtl_quantification_methods_blacklist: list[str] = field(default_factory=lambda: [])
eqtl_lead_pvalue_threshold: float = 1e-3
_target_: str = "gentropy.eqtl_catalogue.EqtlCatalogueStep"


Expand Down Expand Up @@ -169,6 +175,7 @@ class FinngenFinemappingConfig(StepConfig):
_target_: str = (
"gentropy.finngen_finemapping_ingestion.FinnGenFinemappingIngestionStep"
)
finngen_finemapping_lead_pvalue_threshold: float = 1e-5
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There's one thing I'm not sure about. You have added finngen_finemapping_lead_pvalue_threshold to the relevant config, and refer to as pvalue_cutoff=FinngenFinemappingConfig().finngen_finemapping_lead_pvalue_threshold in the step. However, finngen_finemapping_lead_pvalue_threshold it not an argument for FinnGenFinemappingIngestionStep. Is it OK? Would all parameters in the config passed to the step? Would that cause any problem? @project-defiant , what do you think?

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OK, double-checked with @project-defiant and @d0choa and all parameters in the setepConfig classes needs to be parameters in the init function of the step.



@dataclass
Expand Down Expand Up @@ -503,7 +510,6 @@ class StudyLocusValidationStepConfig(StepConfig):
valid_study_locus_path: str = MISSING
invalid_study_locus_path: str = MISSING
invalid_qc_reasons: list[str] = MISSING
gwas_significance: float = WindowBasedClumpingStepConfig.gwas_significance
_target_: str = "gentropy.study_locus_validation.StudyLocusValidationStep"


Expand Down
5 changes: 5 additions & 0 deletions src/gentropy/eqtl_catalogue.py
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Expand Up @@ -3,6 +3,7 @@
from __future__ import annotations

from gentropy.common.session import Session
from gentropy.config import EqtlCatalogueConfig
from gentropy.datasource.eqtl_catalogue.finemapping import EqtlCatalogueFinemapping
from gentropy.datasource.eqtl_catalogue.study_index import EqtlCatalogueStudyIndex

Expand Down Expand Up @@ -61,6 +62,10 @@ def __init__(
credible_sets = EqtlCatalogueFinemapping.from_susie_results(processed_susie_df)
study_index = EqtlCatalogueStudyIndex.from_susie_results(processed_susie_df)

credible_sets = credible_sets.validate_lead_pvalue(
pvalue_cutoff=EqtlCatalogueConfig().eqtl_lead_pvalue_threshold
)

# Load
study_index.df.write.mode(session.write_mode).parquet(
eqtl_catalogue_study_index_out
Expand Down
4 changes: 4 additions & 0 deletions src/gentropy/finngen_finemapping_ingestion.py
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Expand Up @@ -37,6 +37,10 @@ def __init__(
finngen_susie_finemapping_cs_summary_files=finngen_susie_finemapping_cs_summary_files,
)

finngen_finemapping_df = finngen_finemapping_df.validate_lead_pvalue(
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Minor stylistic comment, and it is absolutely my preference, but I like to use as few variables as possible:

(
    # Reading Finngen finemapped dataset and convert it to study locus:
    FinnGenFinemapping.from_finngen_susie_finemapping(
        spark=session.spark,
        finngen_susie_finemapping_snp_files=finngen_susie_finemapping_snp_files,
        finngen_susie_finemapping_cs_summary_files=finngen_susie_finemapping_cs_summary_files,
    )
    # Flagging sub-significnat loci:
    .validate_lead_pvalue(
        pvalue_cutoff=FinngenFinemappingConfig().finngen_finemapping_lead_pvalue_threshold
    )
    # Write the output.
    .df.write.mode(session.write_mode).parquet(
        finngen_finemapping_out
    )
)

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Please carefully check, I removed the variables but not sure

pvalue_cutoff=FinngenFinemappingConfig().finngen_finemapping_lead_pvalue_threshold
)

# Write the output.
finngen_finemapping_df.df.write.mode(session.write_mode).parquet(
finngen_finemapping_out
Expand Down
7 changes: 7 additions & 0 deletions src/gentropy/pics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
from __future__ import annotations

from gentropy.common.session import Session
from gentropy.config import WindowBasedClumpingStepConfig
from gentropy.dataset.study_locus import CredibleInterval, StudyLocus
from gentropy.method.pics import PICS

Expand Down Expand Up @@ -31,5 +32,11 @@ def __init__(
picsed_sl = PICS.finemap(study_locus_ld_annotated).filter_credible_set(
credible_interval=CredibleInterval.IS99
)

# Validate lead p-value
picsed_sl = picsed_sl.validate_lead_pvalue(
pvalue_cutoff=WindowBasedClumpingStepConfig().gwas_significance
)

# Write
picsed_sl.df.write.mode(session.write_mode).parquet(picsed_study_locus_out)
2 changes: 0 additions & 2 deletions src/gentropy/study_locus_validation.py
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Expand Up @@ -19,7 +19,6 @@ def __init__(
session: Session,
study_index_path: str,
study_locus_path: list[str],
gwas_significance: float,
valid_study_locus_path: str,
invalid_study_locus_path: str,
invalid_qc_reasons: list[str] = [],
Expand All @@ -30,7 +29,6 @@ def __init__(
session (Session): Session object.
study_index_path (str): Path to study index file.
study_locus_path (list[str]): Path to study locus dataset.
gwas_significance (float): GWAS significance threshold.
valid_study_locus_path (str): Path to write the valid records.
invalid_study_locus_path (str): Path to write the output file.
invalid_qc_reasons (list[str]): List of invalid quality check reason names from `StudyLocusQualityCheck` (e.g. ['SUBSIGNIFICANT_FLAG']).
Expand Down
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