Common mass spectrometry and statistical tools.

`install.packages('MSbox')`

examples:

```
E_iso('C') # element symbol, case insensitive
E_iso('Carbon') # element full name, case insensitive
E_iso('carBon') # element full name, case insensitive
```

If the queried information is not found for a compounds, it will assign “unknown” to that compound information:

```
describe('malic acid') # get formula by default
describe(c('malic acid', 'citric acid', 'tartaric acid'), representation = "smiles") # get smiles
```

It accepts two types of inputs:

**Standards elemental composition**, for instance,`C7H6O`

,`C7H6Na`

. Here each element is distinguished by Capital letters, i.e., sodium should be written as Na, not NA, na or nA here. Since there is only one sodium in the formula`C7H7Na`

, you don’t have to write 1 after`Na`

.**User friendly elemental composition**, for instance,`c7H6O1`

,`C7H6NA1`

. Here each element is distinguished by the number of the element, therefore, i.e, sodium can be written as`Na`

,`NA`

or`na`

. But the number the sodium element should be clearlly stated in the formula even if there is only one sodium.

example for **Standards elemental composition**:

```
mass("C7H6O", caseSensitive = T)
mass(c("C7H6O", "C7H6Na"), caseSensitive = T) # vector input
```

example for **User friendly elemental composition**:

```
mass("c7h6O1")
mass(c("c7h6o1", "C7H6NA1")) # vector input
```

It accepts two types of inputs:

**Standards elemental composition**, for instance,`C7H6O`

,`C7H6Na`

. Here each element is distinguished by Capital letters, i.e., sodium should be written as Na, not NA, na or nA here. Since there is only one sodium in the formula`C7H7Na`

, you don’t have to write 1 after`Na`

.**User friendly elemental composition**, for instance,`c7H6O1`

,`C7H6NA1`

. Here each element is distinguished by the number of the element, therefore, i.e, sodium can be written as`Na`

,`NA`

or`na`

. But the number the sodium element should be clearlly stated in the formula even if there is only one sodium.

example for **Standards elemental composition**

```
mz("C7H7O", 1, caseSensitive = T) # [M+H]+, positive ion mode, charge z = 1
mz("C7H5O", -1, caseSensitive = T) # [M-H]-, negative ion mode, charge z = 1
mz(c("C7H6O", "C7H6Na"), 1, caseSensitive = T) # vector input
```

example for **User friendly elemental composition**:

```
mz("c7h7O1") # [M+H]+, positive ion mode, charge z = 1
mz("c7H5o", -1) # [M-H]-, negative ion mode, charge z = 1
mz(c("c7h6o1", "C7H6NA1"), 1) # vector input
```

example:

```
ppm(155.03383, 155.03388) # standard way
ppm(155.03383, .03388) # lazy input when the integer parts of m and t are the same
ppm(155.03383, .03388, lazy = F) # lazy input disabled
ppm(155.03384, mz('C7H7O4', z = 1)) # with ion formula
```

example

`Iso_mass(F = 'C7H6O4', iso = '[13]C2[2]H3') # Two 13C and three 2H are labled. Case insensitive.`

example

`Iso_mz(F = 'C7H6O4', iso = '[13]C2[2]H3', z = 1) # Two 13C and three 2H are labled. Case insensitive.`

examples

```
contam(33.0335, ppm = 10, mode = '+')
contam(44.998, ppm = 10, mode = '-')
```

examples

```
adduct('C1H4', mode = '-') # case insensitive
adduct('C1H4', mode = '+') # case insensitive
```

```
what(1034.556, mode = "+", ppm = 3) # single m/z value in HMDB database (default)
what(1034.556, mode = "+", ppm = 3, useDB = "KEGG") # single m/z value in KEGG database
what(c(133.014, 191.020), ppm = 10, mode = '-') # batch search
```

```
searchDB(DF, DB, ppm = 5, RT = 0.2, useRT = T) # with RT searching
searchDB(DF, DB, ppm = 5, RT = 0.2, useRT = F) # without RT searching, default
```

Find the samples names which contain the max ion intensity/peak area for each mass feature

Calculate coefficient of variation (CV) for each mass feature among different sample group

Calculate fold change (FC) for each mass feature among different sample group

Calculate p-value for each mass feature among different sample group

Calculate calculate VIP value for each mass feature among different sample group

You can use `Dostat()`

function to get above statistical
analysis.

```
# sample data
<- matrix(runif(2 * 300), ncol = 2, nrow = 300)
dat rownames(dat) <- 1:dim(dat)[1]
<- rep_len(LETTERS[1:3], 300)
myGroup # statistics
<- doStat(dat, Group = myGroup) myResult
```

```
# sample data
<- matrix(runif(2*300), ncol = 2, nrow = 300)
dat <- rep_len(LETTERS[1:3], 300)
Group # PCA
viewPCA(dat, Group = Group, interactive = T) # you can turn on/off interactive plot using interactive = T/F
```

```
# sample data
<- matrix(runif(100*9), ncol = 100, nrow = 27)
dat <- rep_len(LETTERS[1:3], 27)
myGroup <- rep(1:3, each = 9, times = 1)
myBatch <- c(1:27)
mySeq # view TIC
viewTIC(dat, Group = myGroup, Batch = myBatch, resultBy = "Batch")
```

Normalization methods include: (1) LBME: linear baseline normalization based on mean values; (2) LBMD: linear baseline normalization based on median values; (3) PQN: probabilistic quotient normalization; (4) QT: quantile normalization; (5) TIC: total ion current normalization.

```
<- matrix(runif(100*9), ncol = 100, nrow = 10)
dat <- doNormalization(dat, method = "PQN" ) out
```