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Added molar mass for EDCs. Rebuilt renv.
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@lorenzoFabbri
lorenzoFabbri committed Jul 23, 2024
1 parent 0f3e7e0 commit 859f872
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Showing 4 changed files with 465 additions and 420 deletions.
90 changes: 60 additions & 30 deletions R/edcs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,8 @@ edcs_information <- function() {
pubchem_cid = "",
ctd_id = "",
exposome_explorer_id = "",
parental_compound = ""
parental_compound = "",
molar_mass = "" # g/mol, also known as molecular weight
)
.names <- names(template)

Expand All @@ -27,7 +28,8 @@ edcs_information <- function() {
pubchem_cid = "9274",
ctd_id = "C000654497",
exposome_explorer_id = "NA",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 186.2
),
dep = list(
full_name = "diethyl phosphate",
Expand All @@ -37,7 +39,8 @@ edcs_information <- function() {
pubchem_cid = "654",
ctd_id = "C034789",
exposome_explorer_id = "NA",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 154.10
),
detp = list(
full_name = "diethyl thiophosphate",
Expand All @@ -47,17 +50,19 @@ edcs_information <- function() {
pubchem_cid = "3683036",
ctd_id = "C035638",
exposome_explorer_id = "NA",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 169.16
),
dmdtp = list(
full_name = "dimethyl dithiophosphate",
short_name = "DMDTP",
class = "OP pesticide metabolites",
smiles = "CSP(=O)(O)SC",
pubchem_cid = "NA",
pubchem_cid = "36158",
ctd_id = "Unsure",
exposome_explorer_id = "NA",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 158.18
),
dmp = list(
full_name = "dimethyl phosphate",
Expand All @@ -67,7 +72,8 @@ edcs_information <- function() {
pubchem_cid = "13134",
ctd_id = "C007477",
exposome_explorer_id = "NA",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 126.05
),
dmtp = list(
full_name = "dimethyl thiophosphate",
Expand All @@ -77,7 +83,8 @@ edcs_information <- function() {
pubchem_cid = "168140",
ctd_id = "C040340",
exposome_explorer_id = "NA",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 142.12
),
bpa = list(
full_name = "bisphenol A",
Expand All @@ -87,7 +94,8 @@ edcs_information <- function() {
pubchem_cid = "6623",
ctd_id = "C006780",
exposome_explorer_id = "1418",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 228.29
),
etpa = list(
full_name = "ethyl-paraben",
Expand All @@ -97,7 +105,8 @@ edcs_information <- function() {
pubchem_cid = "8434",
ctd_id = "C012313",
exposome_explorer_id = "1422",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 166.17
),
mepa = list(
full_name = "methyl-paraben",
Expand All @@ -107,7 +116,8 @@ edcs_information <- function() {
pubchem_cid = "7456",
ctd_id = "C015358",
exposome_explorer_id = "1421",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 152.15
),
bupa = list(
full_name = "n‑butyl‑paraben",
Expand All @@ -117,7 +127,8 @@ edcs_information <- function() {
pubchem_cid = "7184",
ctd_id = "C038091",
exposome_explorer_id = "1424",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 194.23
),
oxbe = list(
full_name = "oxybenzone",
Expand All @@ -127,7 +138,8 @@ edcs_information <- function() {
pubchem_cid = "4632",
ctd_id = "C005290",
exposome_explorer_id = "1419",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 228.24
),
prpa = list(
full_name = "propyl-paraben",
Expand All @@ -137,7 +149,8 @@ edcs_information <- function() {
pubchem_cid = "7175",
ctd_id = "C006068",
exposome_explorer_id = "1423",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 180.20
),
trcs = list(
full_name = "triclosan",
Expand All @@ -147,7 +160,8 @@ edcs_information <- function() {
pubchem_cid = "5564",
ctd_id = "D014260",
exposome_explorer_id = "1420",
parental_compound = "NA"
parental_compound = "NA",
molar_mass = 289.5
),
mbzp = list(
full_name = "mono benzyl phthalate",
Expand All @@ -157,7 +171,8 @@ edcs_information <- function() {
pubchem_cid = "31736",
ctd_id = "C103325",
exposome_explorer_id = "1397",
parental_compound = "BBzP"
parental_compound = "BBzP",
molar_mass = 256.25
),
mecpp = list(
full_name = "mono‑2‑ethyl 5‑carboxypentyl phthalate",
Expand All @@ -167,7 +182,8 @@ edcs_information <- function() {
pubchem_cid = "148386",
ctd_id = "C051450",
exposome_explorer_id = "1403",
parental_compound = "DEHP"
parental_compound = "DEHP",
molar_mass = 308.33
),
mehhp = list(
full_name = "mono‑2‑ethyl‑5‑hydroxyhexyl phthalate",
Expand All @@ -177,7 +193,8 @@ edcs_information <- function() {
pubchem_cid = "170295",
ctd_id = "C479069",
exposome_explorer_id = "1402",
parental_compound = "DEHP"
parental_compound = "DEHP",
molar_mass = 294.34
),
meohp = list(
full_name = "mono‑2‑ethyl‑5‑oxohexyl phthalate",
Expand All @@ -187,7 +204,8 @@ edcs_information <- function() {
pubchem_cid = "119096",
ctd_id = "C080276",
exposome_explorer_id = "1401",
parental_compound = "DEHP"
parental_compound = "DEHP",
molar_mass = 292.33
),
mehp = list(
full_name = "mono‑2‑ethylhexyl phthalate",
Expand All @@ -197,7 +215,8 @@ edcs_information <- function() {
pubchem_cid = "21924291",
ctd_id = "C016599",
exposome_explorer_id = "Unsure",
parental_compound = "DEHP"
parental_compound = "DEHP",
molar_mass = 277.33
),
ohminp = list(
full_name = "mono‑4‑methyl‑7‑hydroxyoctyl phthalate",
Expand All @@ -207,7 +226,8 @@ edcs_information <- function() {
pubchem_cid = "102401880",
ctd_id = "NA",
exposome_explorer_id = "1451",
parental_compound = "MiNP"
parental_compound = "MiNP",
molar_mass = 308.4
),
oxominp = list(
full_name = "mono‑4‑methyl‑7‑oxooctyl phthalate",
Expand All @@ -217,7 +237,8 @@ edcs_information <- function() {
pubchem_cid = "102401881",
ctd_id = "NA",
exposome_explorer_id = "1492",
parental_compound = "MiNP"
parental_compound = "MiNP",
molar_mass = 306.4
),
mibp = list(
full_name = "mono‑iso‑butyl phthalate",
Expand All @@ -227,7 +248,8 @@ edcs_information <- function() {
pubchem_cid = "92272",
ctd_id = "C575690",
exposome_explorer_id = "1399",
parental_compound = "DiBP"
parental_compound = "DiBP",
molar_mass = 222.24
),
mnbp = list(
full_name = "mono‑n‑butyl phthalate",
Expand All @@ -237,7 +259,8 @@ edcs_information <- function() {
pubchem_cid = "8575",
ctd_id = "C028577",
exposome_explorer_id = "1398",
parental_compound = "DnBP"
parental_compound = "DnBP",
molar_mass = 222.24
),
mep = list(
full_name = "monoethyl phthalate",
Expand All @@ -247,18 +270,25 @@ edcs_information <- function() {
pubchem_cid = "75318",
ctd_id = "C581825",
exposome_explorer_id = "1396",
parental_compound = "DEP"
parental_compound = "DEP",
molar_mass = 194.18
)
)

edcs_info_df <- stack(edcs_info)
edcs_info_df$col_names <- .names
edcs_info_df <- tidylog::pivot_wider(edcs_info_df,
names_from = col_names,
values_from = values
edcs_info_df <- tidylog::pivot_wider(
edcs_info_df,
names_from = col_names,
values_from = values
)
edcs_info_df <- tidylog::rename(edcs_info_df,
chem_id = ind
edcs_info_df <- tidylog::rename(
edcs_info_df,
chem_id = ind
)

assertthat::assert_that(
length(unique(edcs_info_df$pubchem_cid)) == length(edcs_info_df$pubchem_cid)
)

return(edcs_info_df)
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