iCellR (version 1.6.7)

run.cca: Run CCA on the main data

Description

This function takes an object of class iCellR and runs CCA using Seurat.

Usage

run.cca(
  x = NULL,
  top.vari.genes = 1000,
  cc.number = 30,
  dims.align = 1:20,
  normalize.data = TRUE,
  scale.data = TRUE,
  normalization.method = "LogNormalize",
  scale.factor = 10000,
  display.progress = TRUE
)

Value

An object of class iCellR.

Arguments

x

An object of class iCellR.

top.vari.genes

Chose top genes to use for CCA, default = 1000.

cc.number

Choose a number, default = 30.

dims.align

Choose the CCA dimentions to align, default = 1:20.

normalize.data

TRUE or FALSE, default = TRUE.

scale.data

TRUE or FALSE, default = TRUE.

normalization.method

Choose a method, default = "LogNormalize".

scale.factor

Scaling factor, default = 10000.

display.progress

Show progress, default = TRUE.