Function that interrogates and analyzes a list of human protein-coding genes for cancer relevance
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | onco_enrich(
query,
query_id_type = "symbol",
ignore_id_err = FALSE,
project_title = "Project title",
project_owner = "Project owner",
project_description = "Project description",
bgset = NULL,
bgset_id_type = "symbol",
bgset_description = "All protein-coding genes",
p_value_cutoff_enrichment = 0.05,
p_value_adjustment_method = "BH",
q_value_cutoff_enrichment = 0.2,
min_geneset_size = 10,
max_geneset_size = 500,
min_subcellcomp_confidence = 1,
simplify_go = F,
ppi_add_nodes = 50,
ppi_score_threshold = 900,
show_ppi = T,
show_drugs_in_ppi = F,
show_disease = T,
show_drug = T,
show_enrichment = T,
show_tcga_aberration = T,
show_tcga_coexpression = T,
show_cell_tissue = T,
show_unknown_function = T,
show_prognostic_cancer_assoc = T,
show_subcell_comp = T,
show_crispr_lof = T,
show_complex = T
)
|
query |
character vector with gene/query identifiers |
query_id_type |
character indicating source of query (one of "uniprot_acc", "symbol", "entrezgene", or "ensembl_gene_id") |
ignore_id_err |
logical indicating if analysis should continue when uknown query identifiers are encountered |
project_title |
project title (title of report) |
project_owner |
name of project owner |
project_description |
project background information |
bgset |
character vector with gene identifiers, used as reference/background for enrichment/over-representation analysis |
bgset_id_type |
character indicating source of background ("uniprot_acc","symbol","entrezgene","ensembl_gene_id") |
bgset_description |
character indicating type of background (e.g. "All lipid-binding proteins (n = 200)") |
p_value_cutoff_enrichment |
cutoff p-value for enrichment/over-representation analysis |
p_value_adjustment_method |
one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" |
q_value_cutoff_enrichment |
cutoff q-value for enrichment analysis |
min_geneset_size |
minimal size of geneset annotated by term for testing in enrichment/over-representation analysis |
max_geneset_size |
maximal size of geneset annotated by term for testing in enrichment/over-representation analysis |
min_subcellcomp_confidence |
minimum confidence level of subcellular compartment annotations (range from 1 to 6, 6 is strongest) |
simplify_go |
remove highly similar GO terms in results from GO enrichment/over-representation analysis |
ppi_add_nodes |
number of nodes to add to target set when computing the protein-protein interaction network (STRING) |
ppi_score_threshold |
minimum score (0-1000) for retrieval of protein-protein interactions (STRING) |
show_ppi |
logical indicating if report should contain protein-protein interaction data (STRING) |
show_drugs_in_ppi |
logical indicating if targeted drugs (> phase 3) should be displayed in protein-protein interaction network (Open Targets Platform) |
show_disease |
logical indicating if report should contain disease associations (Open Targets Platform) |
show_enrichment |
logical indicating if report should contain functional enrichment/over-representation analysis (MSigDB, GO, KEGG, REACTOME etc.) |
show_tcga_aberration |
logical indicating if report should contain TCGA aberration plots (amplifications/deletions) |
show_tcga_coexpression |
logical indicating if report should contain TCGA co-expression data (RNAseq) of queryset with oncogenes/tumor suppressor genes |
show_unknown_function |
logical indicating if report should highlight target genes with unknown or poorly defined functions |
show_prognostic_cancer_assoc |
logical indicating if mRNA-based (single-gene) prognostic associations to cancer types should be listed |
show_subcell_comp |
logical indicating if report should list subcellular compartment annotations (ComPPI) |
show_crispr_lof |
logical indicating if report should list results from CRISPR/Cas9 loss-of-fitness screens (Project Score) |
show_complex |
logical indicating if report should list proteins in known protein complexes (CORUM) |
show_tissue_cell |
logical indicating if report should contain tissue-specificity and single cell-type specificity assessments of target genes, using data from the Human Protein Atlas |
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