anClique: 'anClique-class' for annotating isotopes and adducts

In cliqueMS: Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

Description

S3 Class anClique-class for annotating isotopes and adducts in processed m/z data. Features are first grouped based on a similarity network algorithm and then annotation of isotopes and adducts is performed in each group.

Usage

anClique

Format

An object of class anClique of length 7.

Details

anClique-class contains the following elements:

'peaklist' Is a data.frame with m/z, retention time and intensity information for each feature. It also contains adduct and isotope information if annotation has been performed.

'network' Is an igraph undirected network of similarity used to compute groups of features before annotation.

'cliques' Is a list that contains the groups of features. Each id corresponds to a row in the peaklist.

'isotopes' Is a data.frame with the column 'feature' for feature id, column 'charge' for the charge, column 'grade' that starts with 0 and it is 1 for the first isotope, 2 for the second and so on and column 'cluster' which labels each group of features that are isotopes.

'cliquesFound' is TRUE if clique groups have been computed, 'isoFound' is TRUE if isotopes have been annotated, 'anFound' is TRUE if annotation of adducts have been computed.

See Also

anClique

cliqueMS documentation built on May 1, 2019, 6:32 p.m.