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Prepare Query Data for Usage Fitting

Source: R/nmf_refit.R
prepare_query.Rd

Prepares query expression data by:

  1. Finding genes overlapping with reference

  2. Validating data properties (non-negative, integer counts)

  3. Scaling columns by standard deviation (without centering)

The scaling step matches the preprocessing in Python starCAT: sklearn.preprocessing.scale(X, with_mean=False)

Usage

prepare_query(query, ref_genes, verbose = TRUE)

Arguments

query

Query matrix (cells x genes)

ref_genes

Gene names in the reference

verbose

Print progress messages

Value

List with:

matrix

Processed query matrix

overlap_genes

Character vector of overlapping gene names