mbecReportPrelim: Constructs an initial report of a single data-set without...

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

Description

Input can be of class MbecData, phyloseq or list(counts, meta-data). The function will check if required covariates are present and apply normalization with default parameters according to chosen type, i.e., 'clr' (cumulative log-ratio) or 'tss' (total sum scaled).

Usage

mbecReportPrelim(
  input.obj,
  model.vars = c("batch", "group"),
  type = "clr",
  return.data = FALSE
)

Arguments

input.obj	list of phyloseq objects to compare, first element is considered uncorrected data
model.vars	required covariates to build models
type	One of 'otu', 'tss' or 'clr' to determine the abundance matrix to use for evaluation.
return.data	TRUE will return a list of all produced plots, FALSE will start rendering the report

Value

either a ggplot2 object or a formatted data-frame to plot from

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