iba: iCellR Batch Alignment (IBA)

In iCellR: Analyzing High-Throughput Single Cell Sequencing Data

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".

iCellR documentation built on Oct. 9, 2021, 5:07 p.m.