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.
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 )
An object of class Seurat.
Name of Assay PRTB signature is being calculated on.
Features to compute PRTB signature for. Defaults to the variable features set in the assay specified.
Data slot to use for PRTB signature calculation.
Metadata column containing target gene classification.
Non-targeting gRNA cell classification identity.
Provide metadata column if multiple biological replicates exist to calculate PRTB signature for every replicate separately.
Number of nearest neighbors to consider.
Reduction method used to calculate nearest neighbors.
Number of dimensions to use from dimensionality reduction method.
Name for the new assay.
Display progress + messages
Returns a Seurat object with a new assay added containing the perturbation signature for all cells in the data slot.