Description Usage Arguments Details Value Author(s) Examples

Wrapper function for the xcms diffreport and the annotate function. Returns a diffreport within the annotation results.

1 2 3 4 5 6 | ```
annotateDiffreport(object, sample=NA, nSlaves=1, sigma=6, perfwhm=0.6,
cor_eic_th=0.75, cor_exp_th = 0.75, graphMethod="hcs", pval=0.05, calcCiS=TRUE,
calcIso=FALSE, calcCaS=FALSE, maxcharge=3, maxiso=4, minfrac=0.5,
ppm=5, mzabs=0.015, quick=FALSE, psg_list=NULL, rules=NULL,
polarity="positive", multiplier=3, max_peaks=100, intval="into",
pval_th = NULL, fc_th = NULL, sortpval=TRUE, ...)
``` |

`object` |
xcmsSet with peak group assignments |

`sample` |
xsAnnotate: Sample selection for grouped xcmsSet, see xsAnnotate-class |

`nSlaves` |
xsAnnotate: Use parallel CAMERA mode, require Rmpi |

`sigma` |
groupFWHM: multiplier of the standard deviation |

`perfwhm` |
groupFWHM: percentage of FWHM width |

`cor_eic_th` |
groupCorr: Correlation threshold for EIC correlation (0..1) |

`cor_exp_th` |
groupCorr: Threshold for intensity correlations across samples (0..1) |

`graphMethod` |
groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra |

`pval` |
groupCorr: significant correlation threshold |

`calcCiS` |
groupCorr: Use correlation inside samples for peak grouping |

`calcIso` |
groupCorr: Use isotopic relationship for peak grouping |

`calcCaS` |
groupCorr: Use correlation across samples for peak grouping |

`maxcharge` |
findIsotopes: max. ion charge |

`maxiso` |
findIsotopes: max. number of expected isotopes |

`minfrac` |
findIsotopes: The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation |

`ppm` |
General ppm error |

`mzabs` |
General absolut error in m/z |

`quick` |
Use only groupFWHM and findIsotopes |

`psg_list` |
Calculation will only be done for the selected groups |

`rules` |
findAdducts: User defined ruleset |

`polarity` |
findAdducts: Which polarity mode was used for measuring of the ms sample |

`multiplier` |
findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions |

`max_peaks` |
How much peaks will be calculated in every thread using the parallel mode |

`intval` |
General used intensity value (into, maxo, intb) |

`pval_th` |
pval threshold. Creates a new psg_list. A pseudospectra is selected if it contains peaks, with pval < pval_th |

`fc_th` |
Same as pval. Select those groups with contains peaks with fold-change > fc_th. Pval_th and fc_th can be combined |

`sortpval` |
Sort diffreport after pvalues |

`...` |
Diffreport parameters see diffreport |

Batch script wrapper for combining the annotation and the diffreport for a (grouped) xcmsSet `xs`

.
Function list: 1: diffreport(), 2: groupFWHM(), 3: findIsotopes(), 4: groupCorr(), 5: findAdducts()
For a speedup calculation users can create a quick run, with quick = TRUE to preselect pseudospectra of interest.
The indices of those pseudospectra are set with psg_list in a second run.
On the other hand, a automatic selection with pval_th and/or fc_th can be performed.
Returns the normal xcms diffreport table, with the additional CAMERA slots

`annotateDiffreport`

returns an diffreport, see diffreport, within additional columns containing the annotation results.

Carsten Kuhl <ckuhl@ipb-halle.de>

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
#Multiple sample
library(CAMERA)
library(faahKO)
xs.grp <- group(faahko)
xs.fill <- fillPeaks(xs.grp)
#fast preselection
# diffreport <- annotateDiffreport(xs.fill,quick=TRUE)
# index <- c(1,18,35,45,56) #Make only for those grps a adduct annotation
# diffreport2 <- annotateDiffreport(xs.fill,psg_list=index,metlin = TRUE)
#automatic selection for groups with peaks p-val < 0.05 and fold-change > 3
# diffreport <- annotateDiffreport(xs.fill,pval_th=0.05,fc=3)
``` |

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