subtract_baseline {autonomics}R Documentation

Subtract baseline

Description

Subtract baseline level within block

Usage

subtract_baseline(
  object,
  subgroupvar,
  subgroupctr = slevels(object, subgroupvar)[1],
  block = NULL,
  assaynames = setdiff(assayNames(object), "weights"),
  verbose = TRUE
)

subtract_pairs(
  object,
  subgroupvar,
  subgroupctr = slevels(object, subgroupvar)[1],
  block,
  assaynames = setdiff(assayNames(object), "weights"),
  verbose = TRUE
)

subtract_differences(object, block, subgroupvar, verbose = TRUE)

Arguments

object

SummarizedExperiment

subgroupvar

subgroup svar

subgroupctr

control subgroup

block

block svar (within which subtraction is performed)

assaynames

which assays to subtract for

verbose

TRUE/FALSE

Details

subtract_baseline subtracts baseline levels within block, using the medoid baseline sample if multiple exist.

subtract_pairs also subtracts baseline level within block. It cannot handle multiple baseline samples, but has instead been optimized for many blocks

subtract_differences subtracts differences between subsequent levels, again within block

Value

SummarizedExperiment

Examples

# read 
    require(magrittr)
    file <- download_data('atkin18.metabolon.xlsx') 
    object0 <- read_metabolon(file, plot=FALSE)
    pca(object0, plot=TRUE, color=SET)

# subtract_baseline: takes medoid of baseline samples if multiple
    object <- subtract_baseline(object0, block='SUB', subgroupvar='SET')
    pca(object, plot=TRUE, color=SET)

# subtract_pairs: optimized for many blocks
    object <- subtract_pairs(   object0, block='SUB', subgroupvar='SET')
    pca(object, plot=TRUE, color=SET)

# subtract differences
    object <- subtract_differences(object0, block='SUB', subgroupvar='SET')
    values(object) %<>% na_to_zero()
    pca(object, plot=TRUE, color=SET)

[Package autonomics version 1.2.0 Index]