Study index dataset from FinnGen.
The following information is aggregated/extracted:
- Study ID in the special format (e.g. FINNGEN_R10_*)
- Trait name (for example, Amoebiasis)
- Number of cases and controls
- Link to the summary statistics location
Some fields are also populated as constants, such as study type and the initial sample size.
Source code in src/gentropy/datasource/finngen/study_index.py
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82 | class FinnGenStudyIndex:
"""Study index dataset from FinnGen.
The following information is aggregated/extracted:
- Study ID in the special format (e.g. FINNGEN_R10_*)
- Trait name (for example, Amoebiasis)
- Number of cases and controls
- Link to the summary statistics location
Some fields are also populated as constants, such as study type and the initial sample size.
"""
finngen_phenotype_table_url: str = "https://r10.finngen.fi/api/phenos"
finngen_release_prefix: str = "FINNGEN_R10"
finngen_summary_stats_url_prefix: str = (
"gs://finngen-public-data-r10/summary_stats/finngen_R10_"
)
finngen_summary_stats_url_suffix: str = ".gz"
@classmethod
def from_source(
cls: type[FinnGenStudyIndex],
spark: SparkSession,
) -> StudyIndex:
"""This function ingests study level metadata from FinnGen.
Args:
spark (SparkSession): Spark session object.
Returns:
StudyIndex: Parsed and annotated FinnGen study table.
"""
json_data = urlopen(cls.finngen_phenotype_table_url).read().decode("utf-8")
rdd = spark.sparkContext.parallelize([json_data])
raw_df = spark.read.json(rdd)
return StudyIndex(
_df=raw_df.select(
f.concat(f.col("phenocode")).alias("studyId"),
f.col("phenostring").alias("traitFromSource"),
f.col("num_cases").cast("integer").alias("nCases"),
f.col("num_controls").cast("integer").alias("nControls"),
(f.col("num_cases") + f.col("num_controls"))
.cast("integer")
.alias("nSamples"),
f.lit(cls.finngen_release_prefix).alias("projectId"),
f.lit("gwas").alias("studyType"),
f.lit(True).alias("hasSumstats"),
f.lit("377,277 (210,870 females and 166,407 males)").alias(
"initialSampleSize"
),
f.array(
f.struct(
f.lit(377277).cast("integer").alias("sampleSize"),
f.lit("Finnish").alias("ancestry"),
)
).alias("discoverySamples"),
# Cohort label is consistent with GWAS Catalog curation.
f.array(f.lit("FinnGen")).alias("cohorts"),
f.concat(
f.lit(cls.finngen_summary_stats_url_prefix),
f.col("phenocode"),
f.lit(cls.finngen_summary_stats_url_suffix),
).alias("summarystatsLocation"),
).withColumn(
"ldPopulationStructure",
StudyIndex.aggregate_and_map_ancestries(f.col("discoverySamples")),
),
_schema=StudyIndex.get_schema(),
)
|
from_source(spark: SparkSession) -> StudyIndex
classmethod
This function ingests study level metadata from FinnGen.
Parameters:
| Name |
Type |
Description |
Default |
spark |
SparkSession
|
|
required
|
Returns:
| Name | Type |
Description |
StudyIndex |
StudyIndex
|
Parsed and annotated FinnGen study table.
|
Source code in src/gentropy/datasource/finngen/study_index.py
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82 | @classmethod
def from_source(
cls: type[FinnGenStudyIndex],
spark: SparkSession,
) -> StudyIndex:
"""This function ingests study level metadata from FinnGen.
Args:
spark (SparkSession): Spark session object.
Returns:
StudyIndex: Parsed and annotated FinnGen study table.
"""
json_data = urlopen(cls.finngen_phenotype_table_url).read().decode("utf-8")
rdd = spark.sparkContext.parallelize([json_data])
raw_df = spark.read.json(rdd)
return StudyIndex(
_df=raw_df.select(
f.concat(f.col("phenocode")).alias("studyId"),
f.col("phenostring").alias("traitFromSource"),
f.col("num_cases").cast("integer").alias("nCases"),
f.col("num_controls").cast("integer").alias("nControls"),
(f.col("num_cases") + f.col("num_controls"))
.cast("integer")
.alias("nSamples"),
f.lit(cls.finngen_release_prefix).alias("projectId"),
f.lit("gwas").alias("studyType"),
f.lit(True).alias("hasSumstats"),
f.lit("377,277 (210,870 females and 166,407 males)").alias(
"initialSampleSize"
),
f.array(
f.struct(
f.lit(377277).cast("integer").alias("sampleSize"),
f.lit("Finnish").alias("ancestry"),
)
).alias("discoverySamples"),
# Cohort label is consistent with GWAS Catalog curation.
f.array(f.lit("FinnGen")).alias("cohorts"),
f.concat(
f.lit(cls.finngen_summary_stats_url_prefix),
f.col("phenocode"),
f.lit(cls.finngen_summary_stats_url_suffix),
).alias("summarystatsLocation"),
).withColumn(
"ldPopulationStructure",
StudyIndex.aggregate_and_map_ancestries(f.col("discoverySamples")),
),
_schema=StudyIndex.get_schema(),
)
|
