calculate_diff: Performing differential analysis on multiple datasets

In desmchoy/BinaryClust: CyTOF Analysis Pipeline Using Binary Classification Followed by Clustering

Performing differential analysis on multiple datasets

Description

This function performs differential analysis on datasets as imported by load_multiple_samples. Returns a list of three data frames: [1] percentage abundances of each cell (sub)type in each sample, [2] log2 fold changes of each cell (sub)type between two conditions and [3] p-values for the fold changes

Usage

calculate_diff(
  multi.data = NULL,
  column = "Cell.Type",
  remove.unclass = FALSE,
  transform = "default"
)

Arguments

multi.data	(Required) A data frame of clustering results. Expects results from load_multi_samples
column	Choose between plotting Cell.Type or Cell.Subtype (Default: Cell.Type)
remove.unclass	Option to remove unclassified cells from plot (Default: FALSE)
transform	Transformation method used for original analysis. 'default' assumes arcsinh transformation. 'none' indicates no transformation (Default: default)

Examples

diff.results <- calculate_diff(multi.data)
diff.results <- calculate_diff(multi.data, transform = 'default', column = 'Cell.Subtype')

desmchoy/BinaryClust documentation built on Sept. 14, 2024, 12:03 a.m.