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