Perform structure/reaction directed analysis for mass only.
getrda(
mz,
pmd = NULL,
freqcutoff = 10,
digits = 3,
top = 20,
formula = NULL,
mdrange = c(0.25, 0.9),
verbose = FALSE
)numeric vector for independent mass or mass to charge ratio. Mass to charge ratio from GlobalStd algorithm is suggested. Isomers would be excluded automated
a specific paired mass distance or a vector of pmds, default NULL
pmd frequency cutoff for structures or reactions, default 10
mass or mass to charge ratio accuracy for pmd, default 3
top n pmd frequency cutoff when the freqcutoff is too small for large data set
vector for formula when you don't have mass or mass to charge ratio data
mass defect range to ignore. Default c(0.25,0.9) to retain the possible reaction related paired mass
logic, if TURE, return will be llist with paired mass distances table. Default FALSE.
logical matrix with row as the same order of mz or formula and column as high frequency pmd group when verbose is FALSE
data(spmeinvivo)
pmd <- getpaired(spmeinvivo)
#> 75 retention time cluster found.
#> 369 paired masses found
#> 5 unique within RT clusters high frequency PMD(s) used for further investigation.
#> The unique within RT clusters high frequency PMD(s) is(are) 28.03 21.98 44.03 17.03 18.01.
#> 719 isotopologue(s) related paired mass found.
#> 492 multi-charger(s) related paired mass found.
std <- getstd(pmd)
#> 8 retention group(s) have single peaks. 14 23 32 33 54 55 56 75
#> 11 group(s) with multiple peaks while no isotope/paired relationship 4 5 7 8 11 41 42 49 68 72 73
#> 9 group(s) with multiple peaks with isotope without paired relationship 2 9 22 26 52 62 64 66 70
#> 4 group(s) with paired relationship without isotope 1 10 15 18
#> 43 group(s) with paired relationship and isotope 3 6 12 13 16 17 19 20 21 24 25 27 28 29 30 31 34 35 36 37 38 39 40 43 44 45 46 47 48 50 51 53 57 58 59 60 61 63 65 67 69 71 74
#> 291 std mass found.
sda <- getrda(spmeinvivo$mz[std$stdmassindex])
#> 15209 pmd found.
#> 3 pmd used.
sda <- getrda(spmeinvivo$mz, pmd = c(2.016,15.995,18.011,14.016))
#> 4 pmd used.