CorMID {CorMID} | R Documentation |

## CorMID.

### Description

`CorMID`

will compute a MID (Mass Isotopomer Distribution)
based on measured ion intensities in GC-APCI-MS.

### Usage

```
CorMID(
int = NULL,
fml = "",
r = NULL,
penalize = 7,
mid_fix = NULL,
trace_steps = FALSE,
prec = 0.01
)
## S3 method for class 'CorMID'
plot(x, ...)
## S3 method for class 'CorMID'
print(x, ...)
```

### Arguments

`int` |
Named numeric vector of measured ion intensities of a fragment. Names will give position of values relative to M+H (see details). |

`fml` |
Chemical formula of the fragment as string. |

`r` |
Either a character vector giving fragments to be considered OR a named numeric giving relative amounts of fragments OR NULL (all known fragments will be estimated) OR a 2-row matrix giving the lower and upper allowed ratio (see examples). |

`penalize` |
Numeric exponent penalizing solutions with low M+H occurrence. Formula is 1+3*(1-x)^penalty. NA to omit penalizing. |

`mid_fix` |
May provide a numeric vector used as a given MID. Allows to estimate |

`trace_steps` |
For testing purposes. Print the results of intermediate steps to console. |

`prec` |
Precision of the estimation of MID, set to 1% as default. |

`x` |
Object of class CorMID. |

`...` |
Further plotting parameters. |

### Details

Let's assume we measured the ion intensities of all 3 isotopes of an
individual compound containing 2 carbons and observe a vector of 978,22,0.
We may calculate the enrichment **E** out of this data, i.e. the relative proportion
of 13C vs total carbon which will amount to about 1.1% (the natural 13C abundance)
under standard conditions.
The equivalent corMID vector would be 1,0,0, indicating that the non-labeled
isotopologue (where non-labeled means non-labeled above the natural 1.1%)
is the only component observed.
During a labeling experiment we may change the measurement values in different
ways (either labeling only one carbon or both), which potentially can translate
into similar values for **E** being larger 1.1%.
The MIDs will provide additional information about the isotopologue fraction
which gave rise to the observed **E**'s (cf. examples). The *r* parameter
indicates an overlay of chemical rearrangements which may occur.

### Value

Estimated percent representation of each isotopologue measured (corMID).

### References

<doi:10.3390/metabo12050408>

### Examples

```
# make up some fake measurement data for Pyruvic acid 2TMS with 3 biological carbon
# assuming 10% labeling at M3 and 2 fragments
fml <- "C9H20O3Si2"
mid <- c(0.9,0,0,0.1)
r <- unlist(list("M+H"=0.8, "M+H2O-CH4"=0.2))
int <- CorMID::recMID(mid=mid, r=r, fml=fml)
plot(int)
# full estimation of M and r
out <- CorMID::CorMID(int=int, fml=fml)
plot(out)
# get an improved result setting r to the correct values
CorMID::CorMID(int=int, fml=fml, r=r, prec=0.0001)
# provoke a wrong estimation using a fixed r
CorMID::CorMID(int=int, fml=fml, r=unlist(list("M+H"=1)))
# calculate r if you know the true corMID for a compound
r <- attr(CorMID::CorMID(int=int, fml=fml, mid_fix=c(0.9,0,0,0.1)), "ratio")
round(CorMID::CorMID(int=int, fml=fml, r=r, prec=0.0001),3)
# deal with missing intensity values
CorMID::CorMID(int=int[-3], fml=fml)
# perform estimation with banded r and observation of optimization steps
r <- matrix(c(0.5,1,0,0.5,0,0.5), nrow=2, dimnames=list(NULL,c("M+H","M+","M+H2O-CH4")))
CorMID::CorMID(int=int, fml=fml, r=r, trace=TRUE)
#process Gln data from publication
utils::data("prep", package = "CorMID")
int <- prep[[24]][["int"]][,6]
fml <- prep[[24]]$fml
CorMID::CorMID(int=int, fml=fml, trace=TRUE)
# check the effect of the penalize parameter on selection of adducts
int <- c(1560, 119203, 41927, 16932, 4438)
names(int) <- c(-2, 0, 1, 2, 3)
fml <- "C19H37NO4Si3"
CorMID::CorMID(int=int, fml=fml, r=NULL, trace=TRUE)
CorMID::CorMID(int=int, fml=fml, r=NULL, trace=TRUE, penalize=7)
```

*CorMID*version 0.1.9 Index]