R/generics.R
, R/components-cliquems.R
generateComponentsCliqueMS.Rd
Uses cliqueMS to generate components using the
cliqueMS::getCliques
function.
generateComponentsCliqueMS(fGroups, ...)
# S4 method for class 'featureGroups'
generateComponentsCliqueMS(
fGroups,
ionization = NULL,
maxCharge = 1,
maxGrade = 2,
ppm = 10,
adductInfo = NULL,
absMzDev = 0.005,
minSize = 2,
relMinAdductAbundance = 0.75,
adductConflictsUsePref = TRUE,
NMConflicts = c("preferential", "mostAbundant", "mostIntense"),
prefAdducts = c("[M+H]+", "[M-H]-"),
extraOptsCli = NULL,
extraOptsIso = NULL,
extraOptsAnn = NULL,
parallel = TRUE
)
# S4 method for class 'featureGroupsSet'
generateComponentsCliqueMS(fGroups, ionization = NULL, ...)
featureGroups
object for which components should be generated.
Further arguments passed to the non-sets workflow method.
Which ionization polarity was used to generate the data: should be "positive"
or "negative"
. If the featureGroups
object has adduct annotations, and ionization=NULL
, the
ionization will be detected automatically.
This parameter is not supported for sets workflows, as the ionization will always be detected automatically.
Arguments passed to cliqueMS::getIsotopes
and/or
cliqueMS::getAnnotation
.
Sets the adinfo
argument to cliqueMS::getAnnotation
.
If NULL
then the default adduct information from cliqueMS is used (i.e. the
positive.adinfo
/negative.adinfo
package datasets).
Maximum absolute m/z deviation.
The minimum size of a component. Smaller components than this size will be removed. See note below.
The minimum relative abundance (0-1) that an adduct should be assigned to
features within the same feature group. See the Feature components
section for more details.
If set to TRUE
, and not all adduct assigments to the features within a feature
group are equal and at least one of those adducts is a preferential adduct (prefAdducts
argument), then only
the features with (the lowest ranked) preferential adduct are considered. In all other cases or when
adductConflictsUsePref=FALSE
only features with the most frequently assigned adduct is considered. See the
Feature components
section for more details.
The strategies to employ when not all neutral masses within a component are equal. Valid options
are: "preferential"
, "mostAbundant"
and "mostIntense"
. Multiple strategies are possible, and
will be executed in the given order until one succeeds. See the Feature components
section for more details.
A character
vector with one or more preferential adducts. See the Feature
components
section for more details.
Named list
with further arguments to be passed to
cliqueMS::getCliques
, cliqueMS::getIsotopes
and cliqueMS::getAnnotation
, respectively. Set to NULL
to ignore.
If set to TRUE
then code is executed in parallel through the futures package. Please
see the parallelization section in the handbook for more details.
A componentsFeatures
derived object.
This function uses cliqueMS to generate components. This function is called when calling generateComponents
with
algorithm="cliquems"
.
The grouping of features in each component ('clique') is based on high similarity of chromatographic elution
profiles. All features in each component are then annotated with the
cliqueMS::getIsotopes
and
cliqueMS::getAnnotation
functions.
The returned components are based on so called feature components. Unlike other algorithms, components are first made on a feature level (per analysis), instead of for complete feature groups. In the final step the feature components are converted to 'regular' components by employing a consensus approach with the following steps:
If an adduct assigned to a feature only occurs as a minority compared to other adduct assigments within the
same feature group, it is considered as an outlier and removed accordingly (controlled by the
relMinAdductAbundance
argument).
For features within a feature group, only keep their adduct assignment if it occurs as the most frequent or
is preferential (controlled by adductConflictsUsePref
and prefAdducts
arguments).
Components are made by combining the feature groups for which at least one of their features are jointly present in the same feature component.
Conflicts of neutral mass assignments within a component (i.e. not all are the same) are dealt with.
Firstly, all feature groups with an unknown neutral mass are split in another component. Then, if conflicts still
occur, the feature groups with similar neutral mass (determined by absMzDev
argument) are grouped. Depending
on the NMConflicts
argument, the group with one or more preferential adduct(s) or that is the largest or
most intense is selected, whereas others are removed from the component. In case multiple groups contain
preferential adducts, and >1 preferential adducts are available, the group with the adduct that matches
first in prefAdducts
'wins'. In case of ties, one of the next strategies in NMConflicts
is tried.
If a feature group occurs in multiple components it will be removed completely.
the minSize
filter is applied.
In a sets workflow the componentization is first performed for each
set independently. The resulting components are then all combined in a componentsSet
object. Note that
the components themselves are never merged. The components are renamed to include the set name from which they were
generated (e.g. "CMP1"
becomes "CMP1-positive"
).
Senan2019patRoon
generateComponents
for more details and other algorithms.