Datasets:
File size: 1,692 Bytes
3c8f60f | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | library(arrow)
library(duckdb)
library(tidyverse)
full_data = arrow::read_parquet("~/code/hf/hackett_2020/hackett_2020.parquet")
con <- duckdb::dbConnect(duckdb::duckdb())
duckdb::duckdb_register_arrow(con, "hackett_meta", arrow::open_dataset("~/code/hf/hackett_2020/hackett_2020.parquet"))
query <- "
WITH regulator_tiers AS (
SELECT
regulator_locus_tag,
CASE
WHEN BOOL_OR(mechanism = 'ZEV' AND restriction = 'P') THEN 1
WHEN BOOL_OR(mechanism = 'GEV' AND restriction = 'P') THEN 2
ELSE 3
END AS tier
FROM hackett_meta
GROUP BY regulator_locus_tag
),
tier_filtered AS (
SELECT
h.*,
t.tier
FROM hackett_meta h
JOIN regulator_tiers t USING (regulator_locus_tag)
WHERE
(t.tier = 1 AND h.mechanism = 'ZEV' AND h.restriction = 'P')
OR (t.tier = 2 AND h.mechanism = 'GEV' AND h.restriction = 'P')
OR (t.tier = 3 AND h.mechanism = 'GEV' AND h.restriction = 'M')
)
SELECT DISTINCT
sample_id,
db_id,
regulator_locus_tag,
regulator_symbol,
target_locus_tag,
target_symbol,
time,
mechanism,
restriction,
date,
strain,
green_median,
red_median,
log2_ratio,
log2_cleaned_ratio,
log2_noise_model,
log2_cleaned_ratio_zth2d,
log2_selected_timecourses,
log2_shrunken_timecourses,
responsive
FROM tier_filtered
WHERE regulator_symbol NOT IN ('GCN4', 'RDS2', 'SWI1', 'MAC1')
"
result <- DBI::dbGetQuery(con, query)
duckdb::dbDisconnect(con)
analysis_set_ids <- result |> distinct(sample_id) |> pull(sample_id)
full_data <- full_data |>
mutate(analysis_set = sample_id %in% analysis_set_ids)
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