inst/scripts/create_adduct_table.R
In rformassspectrometry/MetaboCoreUtils: Core Utils for Metabolomics Data
#' Creating the adduct table from the original adduct list.
#'
create_adduct_table() {
pos <- .adductRulesPos()
neg <- .adductRulesNeg()
add_name <- names(pos)
pos <- do.call(rbind, lapply(unname(pos), as.data.frame))
pos <- cbind(name = add_name, pos, positive = TRUE)
add_name <- names(neg)
neg <- do.call(rbind, lapply(unname(neg), as.data.frame))
neg <- cbind(name = add_name, neg, positive = FALSE)
adds <- rbind(pos, neg)
rownames(adds) <- adds$name
write.table(adds, file = "../adducts/adduct_definition.txt", sep = "\t",
row.names = FALSE)
}
.adductRulesPos <- function() {
## create list with all the adduct definitoins
adduct_list <- list(
# triple charged -----------------------------------------------------------
"[M+3H]3+" = list(mass_multi = 1 / 3,
mass_add = 3 * 1.007276 / 3,
formula_add = "H3",
formula_sub = "C0",
charge = 3),
"[M+2H+Na]3+" = list(mass_multi = 1 / 3,
mass_add = (2 * 1.007276 + 1 * 22.98922) / 3,
formula_add = "H2Na",
formula_sub = "C0",
charge = 3),
"[M+H+Na2]3+" = list(mass_multi = 1 / 3,
mass_add = (1 * 1.007276 + 2 * 22.98922) / 3,
formula_add = "HNa2",
formula_sub = "C0",
charge = 3),
"[M+Na3]3+" = list(mass_multi = 1 / 3,
mass_add = (3 * 22.98922) / 3,
formula_add = "Na3",
formula_sub = "C0",
charge = 3),
# double charged -----------------------------------------------------------
"[M+2H]2+" = list(mass_multi = 1 / 2,
mass_add = 2 * 1.007276 / 2,
formula_add = "H2",
formula_sub = "C0",
charge = 2),
"[M+H+NH4]2+" = list(mass_multi = 1 / 2,
mass_add = (1.007276 + 18.03383) / 2,
formula_add = "NH5",
formula_sub = "C0",
charge = 2),
"[M+H+K]2+" = list(mass_multi = 1 / 2,
mass_add = (1.007276 + 38.96316) / 2,
formula_add = "HK",
formula_sub = "C0",
charge = 2),
"[M+H+Na]2+" = list(mass_multi = 1 / 2,
mass_add = (1.007276 + 22.98922) / 2,
formula_add = "HNa",
formula_sub = "C0",
charge = 2),
"[M+C2H3N+2H]2+"= list(mass_multi = 1 / 2,
mass_add = (2 * 1.007276 + 41.02655) / 2,
formula_add = "C2H5N",
formula_sub = "C0",
charge = 2),
"[M+2Na]2+" = list(mass_multi = 1 / 2,
mass_add = 2 * 22.98922 / 2,
formula_add = "Na2",
formula_sub = "C0",
charge = 2),
"[M+C4H6N2+2H]2+"= list(mass_multi = 1 / 2,
mass_add = (2 * 1.007276 + 2 * 41.02655) / 2,
formula_add = "C4H8N2",
formula_sub = "C0",
charge = 2),
"[M+C6H9N3+2H]2+" = list(mass_multi = 1 / 2,
mass_add = (2 * 1.007276 + 3 * 41.02655) / 2,
formula_add = "C6H11N3",
formula_sub = "C0",
charge = 2),
# single charged -----------------------------------------------------------
"[M+H]+" = list(mass_multi = 1,
mass_add = 1.007276,
formula_add = "H",
formula_sub = "C0",
charge = 1),
"[M+Li]+" = list(mass_multi = 1,
mass_add = 7.015456,
formula_add = "Li",
formula_sub = "C0",
charge = 1),
"[M+2Li-H]+" = list(mass_multi = 1,
mass_add = 2 * 7.015456 - 1.007276,
formula_add = "Li2",
formula_sub = "H",
charge = 1),
"[M+NH4]+" = list(mass_multi = 1,
mass_add = 18.03383,
formula_add = "NH4",
formula_sub = "C0",
charge = 1),
"[M+H2O+H]+" = list(mass_multi = 1,
mass_add = 18.01056 + 1.007276,
formula_add = "H3O",
formula_sub = "C0",
charge = 1),
"[M+Na]+" = list(mass_multi = 1,
mass_add = 22.98922,
formula_add = "Na",
formula_sub = "C0",
charge = 1),
"[M+CH4O+H]+" = list(mass_multi = 1,
mass_add = 1.007276 + 32.02621,
formula_add = "CH5O",
formula_sub = "C0",
charge = 1),
"[M+K]+" = list(mass_multi = 1,
mass_add = 38.96316,
formula_add = "K",
formula_sub = "C0",
charge = 1),
"[M+C2H3N+H]+" = list(mass_multi = 1,
mass_add = 1.007276 + 41.02655,
formula_add = "C2H4N",
formula_sub = "C0",
charge = 1),
"[M+2Na-H]+" = list(mass_multi = 1,
mass_add = 2 * 22.98922 - 1.007276,
formula_add = "Na2",
formula_sub = "H",
charge = 1),
"[M+C3H8O+H]+" = list(mass_multi = 1,
mass_add = 60.05751 + 1.007276,
formula_add = "C3H9O",
formula_sub = "C0",
charge = 1),
"[M+C2H3N+Na]+" = list(mass_multi = 1,
mass_add = 22.98922 + 41.02655,
formula_add = "C2H3NNa",
formula_sub = "C0",
charge = 1),
"[M+2K-H]+" = list(mass_multi = 1,
mass_add = 2 * 38.96316 - 1.007276,
formula_add = "K2",
formula_sub = "H",
charge = 1),
"[M+C2H6OS+H]+" = list(mass_multi = 1,
mass_add = 1.007276 + 78.01394,
formula_add = "C2H7OS",
formula_sub = "C0",
charge = 1),
"[M+C4H6N2+H]+" = list(mass_multi = 1,
mass_add = 1.007276 + 2 * 41.02655,
formula_add = "C4H7N2",
formula_sub = "C0",
charge = 1),
# dimers -------------------------------------------------------------------
"[2M+H]+" = list(mass_multi = 2,
mass_add = 1.007276,
formula_add = "H",
formula_sub = "C0",
charge = 1),
"[2M+NH4]+" = list(mass_multi = 2,
mass_add = 18.03383,
formula_add = "NH4",
formula_sub = "C0",
charge = 1),
"[2M+Na]+" = list(mass_multi = 2,
mass_add = 22.98922,
formula_add = "Na",
formula_sub = "C0",
charge = 1),
"[2M+K]+" = list(mass_multi = 2,
mass_add = 38.96316,
formula_add = "K",
formula_sub = "C0",
charge = 1),
"[2M+C2H3N+H]+" = list(mass_multi = 2,
mass_add = 1.007276 + 41.02655,
formula_add = "C2H4N",
formula_sub = "C0",
charge = 1),
"[2M+C2H3N+Na]+" = list(mass_multi = 2,
mass_add = 22.98922 + 41.02655,
formula_add = "C2H3NNa",
formula_sub = "C0",
charge = 1),
# trimers -------------------------------------------------------------------
"[3M+H]+" = list(mass_multi = 3,
mass_add = 1.007276,
formula_add = "H",
formula_sub = "C0",
charge = 1)
)
## return values
adduct_list
}
.adductRulesNeg <- function() {
## create list with all the adduct definitoins
adduct_list <- list(
# triple charged -----------------------------------------------------------
"[M-3H]3-" = list(mass_multi = 1 / 3,
mass_add = - 3 * 1.007276 / 3,
formula_add = "C0",
formula_sub = "H3",
charge = -3),
# double charged -----------------------------------------------------------
"[M-2H]2-" = list(mass_multi = 1 / 2,
mass_add = - 2 * 1.007276 / 2,
formula_add = "C0",
formula_sub = "H2",
charge = -2),
# single charged -----------------------------------------------------------
"[M-H]-" = list(mass_multi = 1 ,
mass_add = - 1.007276,
formula_add = "C0",
formula_sub = "H",
charge = -1),
"[M+Na-2H]-" = list(mass_multi = 1,
mass_add = - 2 * 1.007276 + 22.98922,
formula_add = "Na",
formula_sub = "H2",
charge = -1),
"[M+Cl]-" = list(mass_multi = 1,
mass_add = 34.9694,
formula_add = "Cl",
formula_sub = "C0",
charge = -1),
"[M+K-2H]-" = list(mass_multi = 1,
mass_add = - 2 * 1.007276 + 38.96316,
formula_add = "K",
formula_sub = "H2",
charge = -1),
"[M+C2H3N-H]-" = list(mass_multi = 1,
mass_add = 41.02655 - 1.007276,
formula_add = "C2H3N",
formula_sub = "H",
charge = -1),
"[M+CHO2]-" = list(mass_multi = 1,
mass_add = 44.9982,
formula_add = "CHO2",
formula_sub = "C0",
charge = -1),
"[M+C2H3O2]-" = list(mass_multi = 1,
mass_add = 59.01385,
formula_add = "C2H3O2",
formula_sub = "C0",
charge = -1),
"[M+Br]-" = list(mass_multi = 1,
mass_add = 78.91889,
formula_add = "Br",
formula_sub = "C0",
charge = -1),
"[M+C2F3O2]-"= list(mass_multi = 1,
mass_add = 112.9856,
formula_add = "C2F3O2",
formula_sub = "C0",
charge = -1),
# dimers -------------------------------------------------------------------
"[2M-H]-" = list(mass_multi = 2,
mass_add = - 1.007276,
formula_add = "C0",
formula_sub = "H",
charge = -1),
"[2M+CHO2]-" = list(mass_multi = 2,
mass_add = 44.9982,
formula_add = "CHO2",
formula_sub = "C0",
charge = -1),
"[2M+C2H3O2]-"= list(mass_multi = 2,
mass_add = 59.01385,
formula_add = "C2H3O2",
formula_sub = "C0",
charge = -1),
# trimers ------------------------------------------------------------------
"[3M-H]-" = list(mass_multi = 3 ,
mass_add = - 1.007276,
formula_add = "C0",
formula_sub = "H",
charge = -1))
## return values
adduct_list
}
rformassspectrometry/MetaboCoreUtils documentation built on Oct. 2, 2024, 5:13 a.m.
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#' Creating the adduct table from the original adduct list.
#'
create_adduct_table() {
pos <- .adductRulesPos()
neg <- .adductRulesNeg()
add_name <- names(pos)
pos <- do.call(rbind, lapply(unname(pos), as.data.frame))
pos <- cbind(name = add_name, pos, positive = TRUE)
add_name <- names(neg)
neg <- do.call(rbind, lapply(unname(neg), as.data.frame))
neg <- cbind(name = add_name, neg, positive = FALSE)
adds <- rbind(pos, neg)
rownames(adds) <- adds$name
write.table(adds, file = "../adducts/adduct_definition.txt", sep = "\t",
row.names = FALSE)
}
.adductRulesPos <- function() {
## create list with all the adduct definitoins
adduct_list <- list(
# triple charged -----------------------------------------------------------
"[M+3H]3+" = list(mass_multi = 1 / 3,
mass_add = 3 * 1.007276 / 3,
formula_add = "H3",
formula_sub = "C0",
charge = 3),
"[M+2H+Na]3+" = list(mass_multi = 1 / 3,
mass_add = (2 * 1.007276 + 1 * 22.98922) / 3,
formula_add = "H2Na",
formula_sub = "C0",
charge = 3),
"[M+H+Na2]3+" = list(mass_multi = 1 / 3,
mass_add = (1 * 1.007276 + 2 * 22.98922) / 3,
formula_add = "HNa2",
formula_sub = "C0",
charge = 3),
"[M+Na3]3+" = list(mass_multi = 1 / 3,
mass_add = (3 * 22.98922) / 3,
formula_add = "Na3",
formula_sub = "C0",
charge = 3),
# double charged -----------------------------------------------------------
"[M+2H]2+" = list(mass_multi = 1 / 2,
mass_add = 2 * 1.007276 / 2,
formula_add = "H2",
formula_sub = "C0",
charge = 2),
"[M+H+NH4]2+" = list(mass_multi = 1 / 2,
mass_add = (1.007276 + 18.03383) / 2,
formula_add = "NH5",
formula_sub = "C0",
charge = 2),
"[M+H+K]2+" = list(mass_multi = 1 / 2,
mass_add = (1.007276 + 38.96316) / 2,
formula_add = "HK",
formula_sub = "C0",
charge = 2),
"[M+H+Na]2+" = list(mass_multi = 1 / 2,
mass_add = (1.007276 + 22.98922) / 2,
formula_add = "HNa",
formula_sub = "C0",
charge = 2),
"[M+C2H3N+2H]2+"= list(mass_multi = 1 / 2,
mass_add = (2 * 1.007276 + 41.02655) / 2,
formula_add = "C2H5N",
formula_sub = "C0",
charge = 2),
"[M+2Na]2+" = list(mass_multi = 1 / 2,
mass_add = 2 * 22.98922 / 2,
formula_add = "Na2",
formula_sub = "C0",
charge = 2),
"[M+C4H6N2+2H]2+"= list(mass_multi = 1 / 2,
mass_add = (2 * 1.007276 + 2 * 41.02655) / 2,
formula_add = "C4H8N2",
formula_sub = "C0",
charge = 2),
"[M+C6H9N3+2H]2+" = list(mass_multi = 1 / 2,
mass_add = (2 * 1.007276 + 3 * 41.02655) / 2,
formula_add = "C6H11N3",
formula_sub = "C0",
charge = 2),
# single charged -----------------------------------------------------------
"[M+H]+" = list(mass_multi = 1,
mass_add = 1.007276,
formula_add = "H",
formula_sub = "C0",
charge = 1),
"[M+Li]+" = list(mass_multi = 1,
mass_add = 7.015456,
formula_add = "Li",
formula_sub = "C0",
charge = 1),
"[M+2Li-H]+" = list(mass_multi = 1,
mass_add = 2 * 7.015456 - 1.007276,
formula_add = "Li2",
formula_sub = "H",
charge = 1),
"[M+NH4]+" = list(mass_multi = 1,
mass_add = 18.03383,
formula_add = "NH4",
formula_sub = "C0",
charge = 1),
"[M+H2O+H]+" = list(mass_multi = 1,
mass_add = 18.01056 + 1.007276,
formula_add = "H3O",
formula_sub = "C0",
charge = 1),
"[M+Na]+" = list(mass_multi = 1,
mass_add = 22.98922,
formula_add = "Na",
formula_sub = "C0",
charge = 1),
"[M+CH4O+H]+" = list(mass_multi = 1,
mass_add = 1.007276 + 32.02621,
formula_add = "CH5O",
formula_sub = "C0",
charge = 1),
"[M+K]+" = list(mass_multi = 1,
mass_add = 38.96316,
formula_add = "K",
formula_sub = "C0",
charge = 1),
"[M+C2H3N+H]+" = list(mass_multi = 1,
mass_add = 1.007276 + 41.02655,
formula_add = "C2H4N",
formula_sub = "C0",
charge = 1),
"[M+2Na-H]+" = list(mass_multi = 1,
mass_add = 2 * 22.98922 - 1.007276,
formula_add = "Na2",
formula_sub = "H",
charge = 1),
"[M+C3H8O+H]+" = list(mass_multi = 1,
mass_add = 60.05751 + 1.007276,
formula_add = "C3H9O",
formula_sub = "C0",
charge = 1),
"[M+C2H3N+Na]+" = list(mass_multi = 1,
mass_add = 22.98922 + 41.02655,
formula_add = "C2H3NNa",
formula_sub = "C0",
charge = 1),
"[M+2K-H]+" = list(mass_multi = 1,
mass_add = 2 * 38.96316 - 1.007276,
formula_add = "K2",
formula_sub = "H",
charge = 1),
"[M+C2H6OS+H]+" = list(mass_multi = 1,
mass_add = 1.007276 + 78.01394,
formula_add = "C2H7OS",
formula_sub = "C0",
charge = 1),
"[M+C4H6N2+H]+" = list(mass_multi = 1,
mass_add = 1.007276 + 2 * 41.02655,
formula_add = "C4H7N2",
formula_sub = "C0",
charge = 1),
# dimers -------------------------------------------------------------------
"[2M+H]+" = list(mass_multi = 2,
mass_add = 1.007276,
formula_add = "H",
formula_sub = "C0",
charge = 1),
"[2M+NH4]+" = list(mass_multi = 2,
mass_add = 18.03383,
formula_add = "NH4",
formula_sub = "C0",
charge = 1),
"[2M+Na]+" = list(mass_multi = 2,
mass_add = 22.98922,
formula_add = "Na",
formula_sub = "C0",
charge = 1),
"[2M+K]+" = list(mass_multi = 2,
mass_add = 38.96316,
formula_add = "K",
formula_sub = "C0",
charge = 1),
"[2M+C2H3N+H]+" = list(mass_multi = 2,
mass_add = 1.007276 + 41.02655,
formula_add = "C2H4N",
formula_sub = "C0",
charge = 1),
"[2M+C2H3N+Na]+" = list(mass_multi = 2,
mass_add = 22.98922 + 41.02655,
formula_add = "C2H3NNa",
formula_sub = "C0",
charge = 1),
# trimers -------------------------------------------------------------------
"[3M+H]+" = list(mass_multi = 3,
mass_add = 1.007276,
formula_add = "H",
formula_sub = "C0",
charge = 1)
)
## return values
adduct_list
}
.adductRulesNeg <- function() {
## create list with all the adduct definitoins
adduct_list <- list(
# triple charged -----------------------------------------------------------
"[M-3H]3-" = list(mass_multi = 1 / 3,
mass_add = - 3 * 1.007276 / 3,
formula_add = "C0",
formula_sub = "H3",
charge = -3),
# double charged -----------------------------------------------------------
"[M-2H]2-" = list(mass_multi = 1 / 2,
mass_add = - 2 * 1.007276 / 2,
formula_add = "C0",
formula_sub = "H2",
charge = -2),
# single charged -----------------------------------------------------------
"[M-H]-" = list(mass_multi = 1 ,
mass_add = - 1.007276,
formula_add = "C0",
formula_sub = "H",
charge = -1),
"[M+Na-2H]-" = list(mass_multi = 1,
mass_add = - 2 * 1.007276 + 22.98922,
formula_add = "Na",
formula_sub = "H2",
charge = -1),
"[M+Cl]-" = list(mass_multi = 1,
mass_add = 34.9694,
formula_add = "Cl",
formula_sub = "C0",
charge = -1),
"[M+K-2H]-" = list(mass_multi = 1,
mass_add = - 2 * 1.007276 + 38.96316,
formula_add = "K",
formula_sub = "H2",
charge = -1),
"[M+C2H3N-H]-" = list(mass_multi = 1,
mass_add = 41.02655 - 1.007276,
formula_add = "C2H3N",
formula_sub = "H",
charge = -1),
"[M+CHO2]-" = list(mass_multi = 1,
mass_add = 44.9982,
formula_add = "CHO2",
formula_sub = "C0",
charge = -1),
"[M+C2H3O2]-" = list(mass_multi = 1,
mass_add = 59.01385,
formula_add = "C2H3O2",
formula_sub = "C0",
charge = -1),
"[M+Br]-" = list(mass_multi = 1,
mass_add = 78.91889,
formula_add = "Br",
formula_sub = "C0",
charge = -1),
"[M+C2F3O2]-"= list(mass_multi = 1,
mass_add = 112.9856,
formula_add = "C2F3O2",
formula_sub = "C0",
charge = -1),
# dimers -------------------------------------------------------------------
"[2M-H]-" = list(mass_multi = 2,
mass_add = - 1.007276,
formula_add = "C0",
formula_sub = "H",
charge = -1),
"[2M+CHO2]-" = list(mass_multi = 2,
mass_add = 44.9982,
formula_add = "CHO2",
formula_sub = "C0",
charge = -1),
"[2M+C2H3O2]-"= list(mass_multi = 2,
mass_add = 59.01385,
formula_add = "C2H3O2",
formula_sub = "C0",
charge = -1),
# trimers ------------------------------------------------------------------
"[3M-H]-" = list(mass_multi = 3 ,
mass_add = - 1.007276,
formula_add = "C0",
formula_sub = "H",
charge = -1))
## return values
adduct_list
}
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