getrda: Perform structure/reaction directed analysis for mass only.

In yufree/pmd: Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis

Perform structure/reaction directed analysis for mass only.

Description

Perform structure/reaction directed analysis for mass only.

Usage

getrda(
  mz,
  pmd = NULL,
  freqcutoff = 10,
  digits = 3,
  top = 20,
  formula = NULL,
  mdrange = c(0.25, 0.9),
  verbose = FALSE
)

Arguments

mz	numeric vector for independent mass or mass to charge ratio. Mass to charge ratio from GlobalStd algorithm is suggested. Isomers would be excluded automated
pmd	a specific paired mass distance or a vector of pmds, default NULL
freqcutoff	pmd frequency cutoff for structures or reactions, default 10
digits	mass or mass to charge ratio accuracy for pmd, default 3
top	top n pmd frequency cutoff when the freqcutoff is too small for large data set
formula	vector for formula when you don't have mass or mass to charge ratio data
mdrange	mass defect range to ignore. Default c(0.25,0.9) to retain the possible reaction related paired mass
verbose	logic, if TURE, return will be llist with paired mass distances table. Default FALSE.

Value

logical matrix with row as the same order of mz or formula and column as high frequency pmd group when verbose is FALSE

See Also

getsda

Examples

data(spmeinvivo)
pmd <- getpaired(spmeinvivo)
std <- getstd(pmd)
sda <- getrda(spmeinvivo$mz[std$stdmassindex])
sda <- getrda(spmeinvivo$mz, pmd = c(2.016,15.995,18.011,14.016))

yufree/pmd documentation built on April 19, 2024, 9:31 a.m.