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ComBat adjusted object

bc_combat.Rd

This function returns a pmart object that has been undergone ComBat batch effect correction

Usage

bc_combat(omicsData, use_groups = FALSE)

Arguments

omicsData

an object of the class 'pepData', 'proData', 'metabData', 'lipidData', or 'nmrData', usually created by as.pepData, as.proData, as.metabData, as.lipidData, or as.nmrData, respectively.

use_groups

logical argument indicating if the group designation should be applied to the data for batch correction. Defaults to FALSE. If TRUE, ComBat runs with both a batch effect and a group designation

Value

Object of same class as omicsData that has been undergone ComBat batch effect correction

Author

Damon Leach

Examples

library(malbacR)
library(pmartR)
data("pmart_amide")
pmart_amide <- edata_transform(pmart_amide,"log2")
pmart_amide <- group_designation(pmart_amide,main_effects = "group",batch_id = "batch")
pmart_amide <- normalize_global(pmart_amide,subset_fn = "all",norm_fn = "median",
                               apply_norm = TRUE,backtransform = TRUE)
amide_combat <- bc_combat(omicsData = pmart_amide, use_groups = FALSE)
#> Found3batches
#> Adjusting for0covariate(s) or covariate level(s)
#> Found3562Missing Data Values 
#> Standardizing Data across genes
#> Fitting L/S model and finding priors
#> Finding parametric adjustments
#> Adjusting the Data