project_query: Project query data onto PCA reference

In powellgenomicslab/scPred: scPred - accurate supervised method for cell-type classification from single-cell RNA-seq data

Description

Projects data from Seurat object onto a pre-computed PCA

Usage

project_query(
  new,
  reference,
  max.iter.harmony = 20,
  recompute_alignment = TRUE,
  seed = 66,
  ...
)

Arguments

new	A Seurat object containing cells to be projected
reference	A Seurat object after running getFeatureSpace()
max.iter.harmony	Maximum number of rounds to run Harmony. One round of Harmony involves one clustering and one correction step.
recompute_alignment	Recompute alignment? Useful if scPredict() has already been run
seed	Numeric seed for harmony
...	Further arguments to HarmonyMatrix()

Value

A Seurat object with two new reductions:

• scpred: Aligned data using harmony

• scpred_projection: Raw projection using reference loadings

Author(s)

José Alquicira Hernández

powellgenomicslab/scPred documentation built on July 16, 2021, 12:14 a.m.