## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ----message = FALSE---------------------------------------------------------- library("MetaboCoreUtils") ls(pos = "package:MetaboCoreUtils") ## ----------------------------------------------------------------------------- library(MetaboCoreUtils) ## ----------------------------------------------------------------------------- adductNames() ## ----------------------------------------------------------------------------- masses <- c(123, 842, 324) mass2mz(masses, adduct = c("[M+H]+", "[M+Na]+")) ## ----------------------------------------------------------------------------- formula2mz(c("C6H12O6", "C8H10N4O2"), adduct = c("[M+H]+", "[M+Na]+")) ## ----------------------------------------------------------------------------- frml <- "Na3C4" frml <- standardizeFormula(frml) frml ## ----------------------------------------------------------------------------- frml <- addElements(frml, "H2O") frml ## ----------------------------------------------------------------------------- frml <- subtractElements(frml, "H") frml ## ----------------------------------------------------------------------------- countElements(frml) ## ----------------------------------------------------------------------------- adductFormula(c("C6H12O6", "C8H10N4O2"), adduct = c("[M+H]+", "[M+Na]+")) ## ----------------------------------------------------------------------------- lipid_masses <- c(760.5851, 762.6007, 762.5280) calculateKmd(lipid_masses) ## ----------------------------------------------------------------------------- lipid_rkmd <- calculateRkmd(lipid_masses) isRkmd(lipid_rkmd) ## ----------------------------------------------------------------------------- rti <- read.table(system.file("retentionIndex", "rti.txt", package = "MetaboCoreUtils"), header = TRUE, sep = "\t") rtime <- read.table(system.file("retentionIndex", "metabolites.txt", package = "MetaboCoreUtils"), header = TRUE, sep = "\t") ## ----------------------------------------------------------------------------- head(rti) ## ----------------------------------------------------------------------------- rtime$rindex_r <- indexRtime(rtime$rtime, rti) ## ----------------------------------------------------------------------------- head(rtime) ## ----------------------------------------------------------------------------- ref <- data.frame(rindex = c(1709.8765, 553.7975), refindex = c(1700, 550)) rtime$rindex_cor <- correctRindex(rtime$rindex_r, ref) ## ----sessioninfo, echo=FALSE-------------------------------------------------- sessionInfo()