custom_filter: Custom Filter Object

In pmartR/pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

Custom Filter Object

Description

This function creates a customFilt S3 object based on user-specified items to filter out of the dataset

Usage

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
)

Arguments

omicsData	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.
e_data_remove	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.
f_data_remove	character vector specifying the names of f_data identifiers to remove from the data. This argument can only be specified with other 'remove' arguments.
e_meta_remove	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.
e_data_keep	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.
f_data_keep	character vector specifying the names of f_data identifiers to keep from the data. This argument can only be specified with other 'keep' arguments.
e_meta_keep	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.

Value

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

Author(s)

Kelly Stratton

Examples

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)

pmartR/pmartR documentation built on April 24, 2024, 10:22 p.m.