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Calculate pval for each gene in synthetic null data

Source: R/calc_null_pval.R
calcNullPval.Rd

Runs a Seurat-based null differential expression analysis for provided synthetic null datasets.

Usage

calcNullPval(
  synthetic_null,
  spatial_coords = NULL,
  normalize = T,
  hvg = NULL,
  seed = 123,
  nCores = 1
)

Arguments

synthetic_null

A matrix (genes x cells), or a list of such matrices representing synthetic null data. If not a list, it will be coerced to a list.

spatial_coords

A data frame, should contain two columns representing X and Y coordinates if using spatial data. Default is NULL.

normalize

Logical; if TRUE (default), apply Seurat's NormalizeData to each dataset. If FALSE, sets assay data directly. Set to false if null data is generated using PCA approximation. It is recommended to provide hvg if normalize is false.

hvg

A list of feaures; will be applied if normalization is set to false.

seed

Numeric; random seed for clustering reproducibility (default: 123).

nCores

An integer. The number of cores to use for parallel processing.

Value

A named list with preprocess data and gene p-values