Description Usage Arguments Value

Match a set of peptides with a Mass Spec

1 2 3 |

`peptides` |
the set of peptides, in bacollite format |

`sample` |
the MS sample data, in bacollite format - three replicates required |

`doplot` |
boolean to say if the fit should be plotted |

`force` |
boolean to say if *all* fits should be calculated, instead of just the good matches |

`vlevel` |
verbose level. 0 means no comments, 3 means full comments |

`corlim` |
threshold for correlation scores |

`laglim` |
threshold for lag scores |

`gauss` |
the level of gaussian smoothing. defaults to NA (no smoothing) |

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`ionlim` |
the fraction of the highest intensity that is used to calculate the scaling limit for ms_align |

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`ignore_warnings` |
whether to ignore the check for the input and calculated mass |

a dataframe holding the following fields:

`hit` |
Whether a match was found for this peptide |

`lag1` |
The lag for sample 1 |

`lag2` |
The lag for sample 2 |

`lag3` |
The lag for sample 3 |

`cor1` |
The correlation coefficient for sample 1 |

`cor2` |
The correlation coefficient for sample 2 |

`cor3` |
The correlation coefficient for sample 3 |

`ion1` |
The proportion of total ions for this peptide in sample 1 |

`ion2` |
The proportion of total ions for this peptide in sample 2 |

`ion3` |
The proportion of total ions for this peptide in sample 3 |

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