CurateData: Curate perturbation dataset (in Seurat object format)

In yanwu2014/perturbLM: A lightweight R package that uses linear models to analyze the effects of chemical/genetic perturbations, conditions, and disease states on single gene expression.

Curate perturbation dataset (in Seurat object format)

Description

Curate perturbation dataset (in Seurat object format)

Usage

CurateData(
  obj,
  guide,
  gene,
  ctrl.gene,
  var.genes,
  dataset.name,
  out.dir,
  dose.val = NULL,
  min.cells = 25,
  batch.col = NULL,
  cell.type.col = NULL,
  nfeature.col = "nFeature_RNA",
  size.factor.col = "nCount_RNA",
  mito.col = "percent.mt",
  nfolds = 5,
  seed = 23,
  export = T
)

Arguments

obj	Input Seurat object to curate
guide	Dictionary or vector defining guide RNA perturbations
gene	Dictionary or vector defining gene targets
ctrl.gene	Control gene target (i.e. NTC, AAVS)
var.genes	Variable genes
dataset.name	Name of curated dataset
out.dir	Directory to write curated dataset
dose.val	Perturbation dose (set to 1 if NULL)
min.cells	Minimum cells per gene perturbation
batch.col	Metadata column containing technical/biological batches
cell.type.col	Metadata column containing cell types
nfeature.col	Metadata column containing number of genes expressed
size.factor.col	Metadata column containing number of total counts
mito.col	Metadata column containing fraction of mitochondrial reads
nfolds	Number of folds to use for test/train splitting
seed	Random seed for defining folds
export	If TRUE, write to file (default: TRUE)

yanwu2014/perturbLM documentation built on Aug. 24, 2023, 2:28 p.m.