filter_insource_ions {mpactr} | R Documentation |
Filter Insource ions
Description
filter_insource_ions()
identifies and removes in-source ion clusters based
on a Pearson correlation threshold. Groups of co-eluting features with
identical retention time are identified and used to generate Pearson
correlation matrices. Clusters with self-similarity greater than the
user-defined cluster_threshold
within these matrices are identified as
likely belonging to a single precursor ion and is associated insource ion.
Highly correlated ions are identified and removed.
copy_object
: mpactr is built on an R6 class-system, meaning it operates on
reference semantics in which data is updated in-place. Compared to a
shallow copy, where only data pointers are copied, or a deep copy, where
the entire data object is copied in memory, any changes to the original
data object, regardless if they are assigned to a new object, result in
changes to the original data object. We recommend using the default
copy_object = FALSE
as this makes for an extremely fast and
memory-efficient way to chain mpactr filters together; however, if you
would like to run the filters individually with traditional R style objects,
you can set copy_object
to TRUE
as shown in the filter examples.
Usage
filter_insource_ions(
mpactr_object,
cluster_threshold = 0.95,
copy_object = FALSE
)
Arguments
mpactr_object |
An |
cluster_threshold |
Cluster threshold for ion deconvolution. Default = 0.95. |
copy_object |
A |
Value
an mpactr_object
Examples
data <- import_data(example("coculture_peak_table.csv"),
example("metadata.csv"),
format = "Progenesis"
)
data_filter <- filter_insource_ions(data,
cluster_threshold = 0.95
)