single_gene_preferences function

Single cell-type gene preferences

Measure enrichment of individual cell-types in a signature matrix.

Internal function as part of tissue_scMappR_internal(). This function takes genes preferentially expressed within a gene list, each cell-type and the background (i.e. all genes within the signature matrix) before completing the cell-type specific enrichment of the inputted gene list on each cell type. This function then returns a table describing the cell-type enrichments (p-value and odds ratio) of each cell-type.

single_gene_preferences(
  hg_short,
  hg_full,
  study_name,
  outDir,
  toSave = FALSE,
  path = NULL
)

Arguments

• hg_short: A list with two objects: a "preferences" and a "genesIn". Preferences is a list of gene symbols over-represented in each cell-type and genesIn were all the inputted genes.
• hg_full: The same as hg_short but for every gene in the signature matrix.
• study_name: Name of output table.
• outDir: Directory where table is outputted.
• toSave: Allow scMappR to write files in the current directory (T/F).
• path: If toSave == TRUE, path to the directory where files will be saved.

Returns

single_gene_preferences A gene-set enrichment table of individual cell-type enrichment.

Examples

# load in signature matrices
data(POA_example)
POA_generes <- POA_example$POA_generes
POA_OR_signature <- POA_example$POA_OR_signature
POA_Rank_signature <- POA_example$POA_Rank_signature
sig <- get_gene_symbol(POA_Rank_signature)
Signature <- POA_Rank_signature
rownames(Signature) <- sig$rowname
genes <- rownames(Signature)[1:60]
heatmap_test <- tissue_scMappR_custom(gene_list = genes, signature_matrix = Signature,
                                      output_directory =  "scMappR_test", toSave = FALSE)
single_preferences <- heatmap_test$single_celltype_preferences