iba function

iCellR Batch Alignment (IBA)

This function takes an object of class iCellR and runs CCCA or CPCA batch alignment.

iba(
  x = NULL,
  dims = 1:30,
  k = 10,
  ba.method = "CPCA",
  method = "base.mean.rank",
  top.rank = 500,
  plus.log.value = 0.1,
  scale.data = TRUE,
  gene.list = "character"
)

Arguments

• x: An object of class iCellR.
• dims: PC dimentions to be used
• k: number of neighboring cells for KNN, default = 10.
• ba.method: Batch alignment method. Choose from "CCCA" and "CPCA", default = "CPCA".
• method: Choose from "base.mean.rank" or "gene.model", default is "base.mean.rank". If gene.model is chosen you need to provide gene.list.
• top.rank: A number. Taking the top genes ranked by base mean, default = 500.
• plus.log.value: A number to add to each value in the matrix before log transformasion to aviond Inf numbers, default = 0.1.
• scale.data: If TRUE the data will be scaled (log2 + plus.log.value), default = TRUE.
• gene.list: A charactor vector of genes to be used for PCA. If "clust.method" is set to "gene.model", default = "my_model_genes.txt".