Perform structure/reaction directed analysis for peaks list.
getsda(
list,
rtcutoff = 10,
corcutoff = NULL,
digits = 2,
accuracy = 4,
freqcutoff = NULL
)a list with mzrt profile
cutoff of the distances in retention time hierarchical clustering analysis, default 10
cutoff of the correlation coefficient, default NULL
mass or mass to charge ratio accuracy for pmd, default 2
measured mass or mass to charge ratio in digits, default 4
pmd frequency cutoff for structures or reactions, default NULL. This cutoff will be found by PMD network analysis when it is NULL.
list with tentative isotope, adducts, and neutral loss peaks' index, retention time clusters.
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 <- getsda(std)
#> PMD frequency cutoff is 9 by PMD network analysis with largest network average distance 7.26 .
#> 8 groups were found as high frequency PMD group.
#> 0 was found as high frequency PMD.
#> 2.02 was found as high frequency PMD.
#> 12 was found as high frequency PMD.
#> 28.03 was found as high frequency PMD.
#> 30.05 was found as high frequency PMD.
#> 42.05 was found as high frequency PMD.
#> 58.04 was found as high frequency PMD.
#> 116.08 was found as high frequency PMD.