mbecSetData: Mbec-Data Setter

In buschlab/MBECS: Evaluation and correction of batch effects in microbiome data-sets

Description

Sets and/or replaces selected feature abundance matrix and handles correct orientation. The argument type determines which slot to access, i.e. the base matrices for un-transformed counts "otu", total sum-scaled counts "tss", cumulative log-ratio transformed counts "clr" and batch effect corrected counts "cor" and assessment vectors "ass". The later two additionally require the use of the argument 'label' that specifies the name within the respective lists of corrections and assessments.

Usage

mbecSetData(
  input.obj,
  new.cnts = NULL,
  type = c("otu", "ass", "cor", "clr", "tss"),
  label = character()
)

Arguments

input.obj	MbecData object to work on.
new.cnts	A matrix-like object with same dimension as 'otu_table' in input.obj.
type	Specify which type of data to add, by using one of 'ass' (Assessement), 'cor' (Correction), 'clr' (Cumulative Log-Ratio) or 'tss' (Total Scaled-Sum).
label	For types 'ass' and 'cor' this sets the name within the lists.

Value

Input object with updated attributes.

Examples

# This will fill the 'tss' slot with the supplied matrix.
MBEC.obj <- mbecSetData(input.obj=dummy.mbec, new.cnts=dummy.list$cnts,
    type='tss')

# This will put the given matrix into the list of corrected counts under the
# name "nameOfMethod".
MBEC.obj <- mbecSetData(input.obj=dummy.mbec, new.cnts=dummy.list$cnts,
    type='cor', label="nameOfMethod")

buschlab/MBECS documentation built on Jan. 21, 2022, 1:27 a.m.