This function creates a customFilt S3 object based on user-specified items to filter out of the dataset
custom_filter(
omicsData,
e_data_remove = NULL,
f_data_remove = NULL,
e_meta_remove = NULL,
e_data_keep = NULL,
f_data_keep = NULL,
e_meta_keep = NULL
)an object of class 'pepData', 'proData', 'metabData',
'lipidData', 'nmrData', or 'seqData', created by as.pepData,
as.proData, as.metabData,
as.lipidData, as.nmrData,
as.seqData, respectively.
character vector specifying the names of the e_data identifiers to remove from the data. This argument can only be specified with other 'remove' arguments.
character vector specifying the names of f_data identifiers to remove from the data. This argument can only be specified with other 'remove' arguments.
character vector specifying the names of the e_meta identifiers to remove from the data. This argument can only be specified with other 'remove' arguments.
character vector specifying the names of the e_data identifiers to keep from the data. This argument can only be specified with other 'keep' arguments.
character vector specifying the names of f_data identifiers to keep from the data. This argument can only be specified with other 'keep' arguments.
character vector specifying the names of the e_meta identifiers to keep from the data. This argument can only be specified with other 'keep' arguments.
An S3 object of class 'customFilt', which is a list with 3 elements for e_data, f_data, and e_meta, specifying which entries should be either kept or removed
library(pmartRdata)
to_filter <- custom_filter(omicsData = metab_object,
e_data_remove = "fumaric acid",
f_data_remove = "Sample_1_Phenotype2_B")
summary(to_filter)
to_filter2 <- custom_filter(omicsData = metab_object,
f_data_keep = metab_object$f_data$SampleID[1:10])
summary(to_filter2)