met.FilterVariable | R Documentation |
met.FilterVariable
filters non-informative variables (i.e., features with very small values, near-constant values, or low repeatability) from the dataset, dependent on the user-specified method for filtering. The function applies a filtering method, ranks the variables within the dataset, and removes variables based on its rank. The final dataset should contain no more than than 5000 variables for effective computing. If more features are present, the IQR filter will be applied to keep only a number of 5000, even if filter = "none"
. Data filtering is performed as part of the data preparation workflow met.read_data
.
met.FilterVariable(
mSetObj = NA,
filter = "none",
remain.num = NULL,
qcFilter = "F",
qc.rsd = 0.25,
all.rsd = NULL
)
mSetObj |
Enter the name of the created mSet object (see |
filter |
(Character) Select an option for unspecific filtering based on the following ranking criteria:
|
remain.num |
(Numerical) Enter the number of variables to keep in your dataset. If
|
qcFilter |
(Logical) Filter the variables based on the relative standard deviation of features in QC samples ( |
qc.rsd |
(Numeric) Define the relative standard deviation cut-off in %. Variables with a RSD greater than this number will be removed from the dataset. It is only necessary to specify this argument if |
all.rsd |
(Numeric or |
The input mSet object with filtered data added at mSetObj$dataSet$filt.
Nicolas T. Wirth mail.nicowirth@gmail.com Technical University of Denmark License: GNU GPL (>= 2)
adapted from FilterVariable
(https://github.com/xia-lab/MetaboAnalystR).
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