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Initialize AnnDatR object for gene clustering (genes as samples)

Source: R/hc_initialize.R
hc_initialize.Rd

hc_initialize() takes three data frames: an expression matrix, gene metadata, and sample metadata. The expression matrix must have genes as rows and samples as columns, with the first column as gene IDs. The gene metadata (obs) must have a column matching the gene IDs in the expression matrix. The sample metadata (var) must have a column matching the sample IDs (column names) in the expression matrix.

Usage

hc_initialize(
  X,
  obs,
  var,
  obs_names_col = "ensembl_id",
  var_names_col = "sample_id"
)

Arguments

X

Expression matrix data frame (genes as rows, samples as columns, first column = gene IDs)

obs

Gene metadata data frame (must contain a column matching gene IDs)

var

Sample metadata data frame (must contain a column matching sample IDs)

obs_names_col

Name of the column in gene metadata to use as gene IDs (default: "ensembl_id")

var_names_col

Name of the column in sample metadata to use as sample IDs (default: "sample_id")

Value

AnnDatR object with genes as samples, ready for clustering