subsetCompMS2: subset compMS2 class object using a vector of spectra names

In WMBEdmands/CompMS2miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

Description

subset compMS2 class object using a vector of spectra names

Usage

subsetCompMS2(object, ...)

Arguments

object	a "compMS2" class object.
specNames	character vector of composite spectrum names.
corrNetworkNodes	logical should all the members of correlation network cluster be returned? (default = FALSE).
rtGroups	logical should all the nodes within the same retention time group also be returned? (default = FALSE).
onlyAdductId	logical should only ESI adduct/in-source fragments which have been identified and are connected to the specNames argument be returned? (default = FALSE). If a features of the specNames argument has no adducts identified then it will be returned in isolation.
nodeOrder	neighbourhood order (see ego function from igraph package) for details. If argument "onlyAdductID" is TRUE then only nodes less than order away from each of the specNames argument will be returned. This occurs after onlyAdductId subset features have been identified. This is performed to reduce complexity of very dense network clusters (default = 2).

Value

a "compMS2" class object with the composite spectra and all metID information removed.

WMBEdmands/CompMS2miner documentation built on May 9, 2019, 10:02 p.m.