scAlignCreateObject: Creates scAlign object

In scAlign: An alignment and integration method for single cell genomics

Description

Creates scAlign object

Usage

scAlignCreateObject(sce.objects, genes.use = NULL, labels = list(),
  pca.reduce = FALSE, pcs.compute = 20, cca.reduce = FALSE,
  ccs.compute = 15, data.use = "scale.data",
  project.name = "scAlignProject")

Arguments

sce.objects	List of Seurat or Matrix objects; sample x feature.
genes.use	Genes to use during PCA/CCA, all genes used as default.
labels	List of labels for each object.
pca.reduce	Initial step of dimensionality be performced by PCA.
pcs.compute	Number of PCs to retrain for alignment.
cca.reduce	Initial step of dimensionality be performced by CCA.
ccs.compute	Number of CCs to retrain for alignment.
data.use	Specificies which data to use from a Seurat object for dimensionality reduction.
project.name	Name for current scAlign project.

Value

Initialized scAlign object

Examples

library(Seurat)
library(SingleCellExperiment)

## Input data, 1000 genes x 100 cells
data = matrix(sample.int(10000, 1000*100, TRUE), 1000, 100)
rownames(data) = paste0("gene", seq_len(1000))
colnames(data) = paste0("cell", seq_len(100))

age    = c(rep("young",50), rep("old",50))
labels = c(c(rep("type1",25), rep("type2",25)), c(rep("type1",25), rep("type2",25)))

ctrl.data = data[,which(age == "young")]
stim.data = data[,which(age == "old")]

ctrlSCE <- SingleCellExperiment(
              assays = list(scale.data = data[,which(age == "young")]))

stimSCE <- SingleCellExperiment(
              assays = list(scale.data = data[,which(age == "old")]))

## Build the scAlign class object and compute PCs
scAlignHSC = scAlignCreateObject(sce.objects = list("YOUNG"=ctrlSCE,
                                                    "OLD"=stimSCE),
                                 labels = list(labels[which(age == "young")],
                                               labels[which(age == "old")]),
                                 pca.reduce = TRUE,
                                 pcs.compute = 50,
                                 cca.reduce = TRUE,
                                 ccs.compute = 15,
                                 project.name = "scAlign_Kowalcyzk_HSC")

scAlign documentation built on April 28, 2020, 6:10 p.m.