compute_ewce_scores_environ: Compute EWCE scores - from environment-stored expression data

In alexandruioanvoda/gwascelltyper: Fast GWAS Enrichment Testing

Compute EWCE scores - from environment-stored expression data

Description

Compute gene-by-celltype specificity matrix with the EWCE score. Code modified from the EWCE package by Skene et al. (2016, DOI 10.3389/fnins.2016.00016). If the expression matrix contains NAs, then this function removes NA-only rows and replaces the remaining NAs with the row average.

Usage

compute_ewce_scores_environ(
  obj,
  number_of_threads = 1,
  col_max_miss = 0.1,
  row_max_miss = 0.1
)

Arguments

obj	Environment object containing an exp (numeric matrix of genes-by-cell-ID) & an annot (dataframe of cell annotations).
number_of_threads	Number of threads to parallelize calculation over. Default = 1.
col_max_miss	Column maximum missingness (default = 0.1)
row_max_miss	Row maximum missingness (default = 0.1)

Value

Matrix

alexandruioanvoda/gwascelltyper documentation built on April 16, 2023, 8:03 p.m.