filter_cv {mpactr} | R Documentation |
Filter Non-reproducible ions
Description
filter_cv()
removes feature ions that are found to be non-reproducible
between technical injection replicates. Reproducibility is assessed via mean
or median coefficient of variation (CV) between technical replicates. As
such, this filter is expecting an input dataset with at least two replicate
injections per sample.
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_cv(mpactr_object, cv_threshold = NULL, cv_param, copy_object = FALSE)
Arguments
mpactr_object |
An |
cv_threshold |
Coefficient of variation threshold. A lower cv_threshold will result in more stringent filtering and higher reproducibility. Recommended values between 0.2 - 0.5. |
cv_param |
Coefficient of variation (CV) statistic to use for filtering Options are "mean" or "median", corresponding to mean and median CV, respectively. |
copy_object |
A |
Value
an mpactr_object
.
Examples
data <- import_data(example("coculture_peak_table.csv"),
example("metadata.csv"),
format = "Progenesis"
)
data_filter <- filter_cv(data,
cv_threshold = 0.01,
cv_param = "mean",
copy_object = TRUE
)
data_filter <- filter_cv(data,
cv_threshold = 0.01,
cv_param = "median",
copy_object = TRUE
)