CalcPerturbSig: Calculate a perturbation Signature
In satijalab/seurat: Tools for Single Cell Genomics

CalcPerturbSig

R Documentation

Calculate a perturbation Signature

Description

Function to calculate perturbation signature for pooled CRISPR screen datasets. For each target cell (expressing one target gRNA), we identified 20 cells from the control pool (non-targeting cells) with the most similar mRNA expression profiles. The perturbation signature is calculated by subtracting the averaged mRNA expression profile of the non-targeting neighbors from the mRNA expression profile of the target cell.

Usage

CalcPerturbSig(
  object,
  assay = NULL,
  features = NULL,
  slot = "data",
  gd.class = "guide_ID",
  nt.cell.class = "NT",
  split.by = NULL,
  num.neighbors = NULL,
  reduction = "pca",
  ndims = 15,
  new.assay.name = "PRTB",
  verbose = TRUE
)

Arguments

`object`	An object of class Seurat.
`assay`	Name of Assay PRTB signature is being calculated on.
`features`	Features to compute PRTB signature for. Defaults to the variable features set in the assay specified.
`slot`	Data slot to use for PRTB signature calculation.
`gd.class`	Metadata column containing target gene classification.
`nt.cell.class`	Non-targeting gRNA cell classification identity.
`split.by`	Provide metadata column if multiple biological replicates exist to calculate PRTB signature for every replicate separately.
`num.neighbors`	Number of nearest neighbors to consider.
`reduction`	Reduction method used to calculate nearest neighbors.
`ndims`	Number of dimensions to use from dimensionality reduction method.
`new.assay.name`	Name for the new assay.
`verbose`	Display progress + messages