annotate_gene_lists {GeneSelectR}

Convert and Annotate Gene Lists

Description

This function converts a list of gene lists to different formats and returns an object of the class AnnotatedGeneLists.

Usage

annotate_gene_lists(
  pipeline_results,
  custom_lists = NULL,
  annotations_ahb,
  format = c("ENTREZ", "ENSEMBL", "SYMBOL")
)

Arguments

pipeline_results

A PipelineResults object containing a named list of data frames.

custom_lists

(optional) A named list of character vectors containing additional user-defined gene sets.

annotations_ahb

A data.frame object containing gene annotations with columns 'gene_id', 'gene_name', and 'entrezid'.

format

The format of the gene list in 'pipeline_results' and 'custom_lists'. This should be one of "ENSEMBL", "ENTREZ", or "SYMBOL".

Value

An object of the class AnnotatedGeneLists, which contains the following components: - @field inbuilt: A list of AnnotatedGeneList objects derived from the 'inbuilt_feature_importance' field of the 'pipeline_results' parameter. - @field permutation: A list of AnnotatedGeneList objects derived from the 'permutation_importance' field of the 'pipeline_results' parameter, if available. Each AnnotatedGeneList object in these lists includes the gene identifiers in different formats (SYMBOL, ENSEMBL, ENTREZID) and is structured to facilitate further analysis and visualization of gene lists. If an error occurs during the conversion or annotation process, a warning message is given and the corresponding list entry will be NULL.

Examples

# Simple Usage with Mock Data
# Create a mock PipelineResults object with minimal data
mock_pipeline_results <- new("PipelineResults",
                             inbuilt_feature_importance = list(
                               "GeneSet1" = data.frame(feature = c("BRCA1", "TP53"))),
                             permutation_importance = list(
                               "GeneSet1" = data.frame(feature = c("BRCA1", "TP53"))))

# Mock annotations data frame
mock_annotations_ahb <- data.frame(gene_id = c("BRCA1", "TP53"),
                                   gene_name = c("BRCA1", "TP53"),
                                   entrezid = c(101, 102))

# Convert and annotate gene lists
annotated_lists <- annotate_gene_lists(mock_pipeline_results,
                                       custom_lists = NULL,
                                       mock_annotations_ahb,
                                       "SYMBOL")
print(annotated_lists)

# Using Custom Gene Lists
# Create custom gene lists
custom_gene_lists <- list("CustomList1" = c("BRCA1", "TP53"))

# Convert and annotate gene lists with custom gene lists included
annotated_lists_custom <- annotate_gene_lists(mock_pipeline_results,
                                              custom_gene_lists,
                                              mock_annotations_ahb,
                                              "SYMBOL")
print(annotated_lists_custom)