pmd (version 0.2.7)

getchain: Get reaction chain for specific mass to charge ratio

Description

Get reaction chain for specific mass to charge ratio

Usage

getchain(
  list,
  diff,
  mass,
  digits = 2,
  accuracy = 4,
  rtcutoff = 10,
  corcutoff = 0.6,
  ppm = 25
)

Value

a list with mzrt profile and reaction chain dataframe

Arguments

list

a list with mzrt profile

diff

paired mass distance(s) of interests

mass

a specific mass for known compound or a vector of masses. You could also input formula for certain compounds

digits

mass or mass to charge ratio accuracy for pmd, default 2

accuracy

measured mass or mass to charge ratio in digits, default 4

rtcutoff

cutoff of the distances in retention time hierarchical clustering analysis, default 10

corcutoff

cutoff of the correlation coefficient, default 0.6

ppm

all the peaks within this mass accuracy as seed mass or formula

Examples

data(spmeinvivo)
# check metabolites of C18H39NO
pmd <- getchain(spmeinvivo,diff = c(2.02,14.02,15.99),mass = 286.3101)
# remove the retention time for mass only data
spmeinvivo$rt <- NULL
pmd <- getchain(spmeinvivo,diff = c(2.02,14.02,15.99),mass = 286.3101)