prepare_tt: Prepare differential gene expression table

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

Prepare differential gene expression table

Description

Prepare differential gene expression table for generate_bootstrap_plots_for_transcriptome or ewce_expression_data.

Usage

prepare_tt(
  tt,
  tt_genecol = NULL,
  ttSpecies,
  output_species,
  method = "homologene",
  verbose = TRUE
)

Arguments

tt	Differential expression table. Can be output of topTable function. Minimum requirement is that one column stores a metric of increased/decreased expression (i.e. log fold change, t-statistic for differential expression etc) and another contains gene symbols.
ttSpecies	The species the differential expression table was generated from.
output_species	Species to convert sct_data and hits to (Default: "human"). See list_species for all available species.
method	R package to use for gene mapping: "gprofiler" : Slower but more species and genes. "homologene" : Faster but fewer species and genes. "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources.
verbose	Print messages.

Value

List of 3 items

NathanSkene/EWCE documentation built on April 10, 2024, 1:02 a.m.