getchain: Get reaction chain for specific mass to charge ratio

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

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
)

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

Value

a list with mzrt profile and reaction chain dataframe

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)

pmd documentation built on April 4, 2025, 2:15 a.m.