This function simplifies the enrichment analysis performed by the excellent tool GprofileR.
artmsEnrichProfiler( x, categorySource = c("GO"), species, background = NA, verbose = TRUE )
(list, data.frame) List of protein ids. It can be anything:
either a list of ids, or you could also send a data.frame and it will find
the columns with the IDs. Is not cool? Multiple list can be also sent
simultaneously, as for example running:
(vector) Resources providing the terms on which the enrichment will be performed. The supported resources by gprofiler are:
(char) Specie code: Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - ’hsapiens’, mouse - ’mmusculus’. Check gProfileR to find out more about supported species.
(vector) gene list to use as background for the enrichment
The enrichment results as provided by gprofiler
This function uses the following
gprofiler arguments as default:
ordered_query = FALSE
significant = TRUE
exclude_iea = TRUE
underrep = FALSE
evcodes = FALSE
region_query = FALSE
max_p_value = 0.05
min_set_size = 0
max_set_size = 0
min_isect_size = 0
correction_method = "analytical" #Options: "gSCS", "fdr", "bonferroni"
hier_filtering = "none"
domain_size = "known" # annotated or known
numeric_ns = ""
png_fn = NULL
include_graph = TRUE
# annotate the MSstats results to get the Gene name data_annotated <- artmsAnnotationUniprot( x = artms_data_ph_msstats_results, columnid = "Protein", species = "human") # Filter the list of genes with a log2fc > 2 filtered_data <- unique(data_annotated$Gene[which(data_annotated$log2FC > 2)]) # And perform enrichment analysis data_annotated_enrich <- artmsEnrichProfiler( x = filtered_data, categorySource = c('KEGG'), species = "hsapiens", background = unique(data_annotated$Gene))#>#>