iba {iCellR}

iCellR Batch Alignment (IBA)

Description

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

Usage

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".