pmd (version 0.2.7)

getrda: 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
)

Value

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

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))