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22_merge_data_deg_test.yml
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22_merge_data_deg_test.yml
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target_default: 22_merge_data_deg_test
include:
- 21_merge_data_dl.yml
packages:
- dplyr
- tidyr
- readr
- dataRetrieval
- openxlsx
sources:
- 22_merge_data_deg_test/src/merge_data_fix_degs.R
- 22_merge_data_deg_test/src/deg_sums.R
targets:
22_merge_data_deg_test:
depends:
- chemicalSummary_deg_meto
- chemicalSummary_deg_acet
- chemicalSummary_conc_deg_meto
- chemicalSummary_conc_deg_acet
- chemicalSummary_bench_deg_meto
- chemicalSummary_bench_deg_acet
chems_missing_toxcast:
command: find_missing_tox(data_file = "data/pesticides.xlsx", parents = chem_crosswalk)
chemicalSummary_deg_meto:
command: get_chem_sum_deg(data_file = "data/pesticides.xlsx", parents = chem_crosswalk, metolachlor = TRUE)
chemicalSummary_deg_acet:
command: get_chem_sum_deg("data/pesticides.xlsx", chem_crosswalk, metolachlor = FALSE)
chemicalSummary_conc_deg_meto:
command: merge_deg_parents(chemicalSummary_conc, chem_crosswalk, metolachlor = TRUE)
chemicalSummary_conc_deg_acet:
command: merge_deg_parents(chemicalSummary_conc, chem_crosswalk, metolachlor = FALSE)
# need to find parent benchmark values for degradates with no toxicity info
#chem_bench_surrogates:
# command: get_chem_sum_deg(data_file = "data/pesticides_bench.xlsx", parents = chem_crosswalk, metolachlor = TRUE)
chems_missing_bench:
command: find_missing_bench("data/pesticides_bench.xlsx", chem_crosswalk)
chemicalSummary_bench_deg_meto:
command: get_bench_sum_deg("data/pesticides_bench.xlsx", chem_crosswalk, metolachlor = TRUE)
chemicalSummary_bench_deg_acet:
command: get_bench_sum_deg("data/pesticides_bench.xlsx", chem_crosswalk, metolachlor = FALSE)
parent_class:
command: get_parent_class(chemicalSummary_conc_deg_meto, chem_info)
parent_sums:
command: sum_by_parents(
deg_parent_ear = chemicalSummary_deg_meto,
deg_parent_conc = chemicalSummary_conc_deg_meto,
deg_parent_bench = chemicalSummary_bench_deg_meto)
parent_sums_nozero:
command: filter_parent_sums(parent_sums)
chnm_to_cas:
command: crosswalk_names(conc_dat = chemicalSummary_conc_deg_meto)
parent_summaries:
command: summarize_parents(parent_sums, classes = parent_class, zeros = FALSE)
parent_summaries_zeros:
command: summarize_parents(parent_sums, classes = parent_class, zeros = TRUE)
# for the degradates that are either acetochlor or metolachlor, look at the
# the relationship between the degradate and parent
# if related to one parent more, choose it.
unclassified_degs:
command: get_unclassified(data_file = "data/pesticides.xlsx", parents = chem_crosswalk)
22_merge_data_deg_test/out/unclassified_degradates.png:
command: plot_unclassified_degs(conc_dat = chemicalSummary_conc, unclassified_degs, out_file = target_name)
# create the "boxplot" fig but use the summed parent + degradates
figures/ms_figures/parent_deg_sums_dotplot.png:
command: plot_deg_sums(all_dat = parent_summaries, top_parents, target_name)