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 clusters found.
#> Using ng = 15
#> 5 unique PMDs retained.
#> The unique within RT clusters high frequency PMD(s) is(are) 28.03 21.98 44.03 17.03 18.01.
#> 409 isotope peaks found.
#> 109 multiple charged isotope peaks found.
#> 251 multiple charged peaks found.
#> 346 paired peaks found.
std <- getstd(pmd)
#> 8 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 ... 42 49 68 72 73
#> 9 group(s) with isotope without paired relationship 2 9 22 26 52 62 64 66 70
#> 4 group(s) with paired without isotope relationship 1 10 15 18
#> 43 group(s) with both paired and isotope relationship 3 6 12 13 16 ... 65 67 69 71 74
#> 292 standard masses identified.
sda <- getrda(spmeinvivo$mz[std$stdmassindex])
#> 14728 pmd found.
#> 3 pmd used.
sda <- getrda(spmeinvivo$mz, pmd = c(2.016,15.995,18.011,14.016))
#> 4 pmd used.