updated cancermine data

inst/templates/crispr_lof.Rmd

@@ -43,8 +43,8 @@ cat('\n')
 htmltools::br()
 
 df_display <- onc_enrich_report[['data']][['loss_of_fitness']][['df']] %>%
-  dplyr::select(symbol, tissue, cmp_link) %>%
-  dplyr::rename(cell_lines = cmp_link) %>%
+  dplyr::select(symbol_link_ps, tissue, cmp_link) %>%
+  dplyr::rename(cell_lines = cmp_link, symbol = symbol_link_ps) %>%
   dplyr::mutate(loss_of_fitness = T)
 
 DT::datatable(df_display, escape = F, extensions=c("Buttons","Responsive"), width = "100%",

man/onco_enrich.md

@@ -0,0 +1,73 @@
+# `onco_enrich`: Function that interrogates and analyzes a list of human protein-coding genes for cancer relevance
+
+## Description
+
+
+ Function that interrogates and analyzes a list of human protein-coding genes for cancer relevance
+
+
+## Usage
+
+```r
+onco_enrich(
+  query,
+  query_source = "symbol",
+  ignore_unknown = FALSE,
+  p_title = "Project Title",
+  p_owner = "Project Owner",
+  background_fname = NULL,
+  background_enrichment = NULL,
+  background_enrichment_source = "symbol",
+  background_enrichment_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,
+  simplify_go = F,
+  ppi_add_nodes = 50,
+  ppi_score_threshold = 900,
+  show_ppi = T,
+  show_drugs_in_ppi = F,
+  show_disease = T,
+  show_enrichment = T,
+  show_tcga_aberration = T,
+  show_tcga_coexpression = T,
+  show_subcell_comp = T,
+  show_crispr_lof = T,
+  show_complex = T
+)
+```
+
+
+## Arguments
+
+Argument      |Description
+------------- |----------------
+```query```     |     character vector with gene/query identifiers
+```query_source```     |     character indicating source of query (one of 'uniprot_acc', 'symbol', 'entrezgene', or 'ensembl_gene_id')
+```ignore_unknown```     |     logical indicating if analysis should continue when uknown query identifiers are encountered
+```p_title```     |     title of report
+```p_owner```     |     name of project owner
+```background_fname```     |     filename for simple text file with project background information, one line per background item
+```background_enrichment```     |     character vector with gene identifiers, used as reference/background for enrichment/over-representation analysis
+```background_enrichment_source```     |     character indicating source of background ('uniprot_acc','symbol','entrezgene','ensembl_gene_id')
+```background_enrichment_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
+```simplify_go```     |     remove highly similar GO terms in results from GO enrichment/over-representation analysis
+```ppi_add_nodes```     |     number of nodes to add to query 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_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)
+