Perform structure/reaction directed analysis for peaks list.

getsda(
list,
rtcutoff = 10,
corcutoff = NULL,
digits = 2,
accuracy = 4,
freqcutoff = NULL
)

## Arguments

list

a list with mzrt profile

rtcutoff

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

corcutoff

cutoff of the correlation coefficient, default NULL

digits

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

accuracy

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

freqcutoff

pmd frequency cutoff for structures or reactions, default NULL. This cutoff will be found by PMD network analysis when it is NULL.

## Value

list with tentative isotope, adducts, and neutral loss peaks' index, retention time clusters.

getpaired,getstd,plotpaired

## Examples

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 <- getsda(std)
#> PMD frequency cutoff is 6 by PMD network analysis with largest network average distance 6.67 .
#> 53 groups were found as high frequency PMD group.
#> 0 was found as high frequency PMD.
#> 1.98 was found as high frequency PMD.
#> 2.01 was found as high frequency PMD.
#> 2.02 was found as high frequency PMD.
#> 6.97 was found as high frequency PMD.
#> 11.96 was found as high frequency PMD.
#> 12 was found as high frequency PMD.
#> 13.98 was found as high frequency PMD.
#> 14.02 was found as high frequency PMD.
#> 14.05 was found as high frequency PMD.
#> 15.99 was found as high frequency PMD.
#> 16.03 was found as high frequency PMD.
#> 19.04 was found as high frequency PMD.
#> 28.03 was found as high frequency PMD.
#> 30.05 was found as high frequency PMD.
#> 31.99 was found as high frequency PMD.
#> 33.02 was found as high frequency PMD.
#> 37.02 was found as high frequency PMD.
#> 42.05 was found as high frequency PMD.
#> 48.04 was found as high frequency PMD.
#> 48.98 was found as high frequency PMD.
#> 49.02 was found as high frequency PMD.
#> 54.05 was found as high frequency PMD.
#> 56.06 was found as high frequency PMD.
#> 56.1 was found as high frequency PMD.
#> 58.04 was found as high frequency PMD.
#> 58.08 was found as high frequency PMD.
#> 58.11 was found as high frequency PMD.
#> 63.96 was found as high frequency PMD.
#> 66.05 was found as high frequency PMD.
#> 68.06 was found as high frequency PMD.
#> 70.04 was found as high frequency PMD.
#> 70.08 was found as high frequency PMD.
#> 74.02 was found as high frequency PMD.
#> 80.03 was found as high frequency PMD.
#> 82.08 was found as high frequency PMD.
#> 88.05 was found as high frequency PMD.
#> 91.1 was found as high frequency PMD.
#> 93.12 was found as high frequency PMD.
#> 94.1 was found as high frequency PMD.
#> 96.09 was found as high frequency PMD.
#> 101.05 was found as high frequency PMD.
#> 108.13 was found as high frequency PMD.
#> 110.11 was found as high frequency PMD.
#> 112.16 was found as high frequency PMD.
#> 116.08 was found as high frequency PMD.
#> 122.15 was found as high frequency PMD.
#> 124.16 was found as high frequency PMD.
#> 126.14 was found as high frequency PMD.
#> 144.18 was found as high frequency PMD.
#> 148.04 was found as high frequency PMD.
#> 150.2 was found as high frequency PMD.
#> 173.18 was found as high frequency PMD.