artmsEnrichProfiler: Enrichment analysis using GprofileR

In kroganlab/artMS: Analytical R tools for Mass Spectrometry

Enrichment analysis using GprofileR

Description

This function simplifies the enrichment analysis performed by the excellent tool GprofileR.

Usage

artmsEnrichProfiler(
  x,
  categorySource = c("GO"),
  species,
  background = NA,
  verbose = TRUE
)

Arguments

x	(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: tmp <- split(enrichment$Gene, enrichment$cl_number, drop= TRUE)
categorySource	(vector) Resources providing the terms on which the enrichment will be performed. The supported resources by gprofiler are: GO (GO:BP, GO:MF, GO:CC): Gene Ontology (see more below) KEGG: Biological pathways REAC: Biological pathways (Reactome) TF: Regulatory motifs in DNA (TRANSFAC TFBS) MI: Regulatory motifs in DNA (miRBase microRNAs) CORUM: protein complexes database HP: Human Phenotype Ontology HPA: Protein databases (Human Protein Atlas) OMIM: Online Mendelian Inheritance in Man annotations: BIOGRID: BioGRID protein-protein interactions The type of annotations for Gene Ontology: Inferred from experiment (IDA, IPI, IMP, IGI, IEP) Direct assay (IDA) / Mutant phenotype (IMP] Genetic interaction (IGI) / Physical interaction (IPI) Traceable author (TAS) / Non-traceable author (NAS) / Inferred by curator (IC) Expression pattern (IEP) / Sequence or structural similarity (ISS) / Genomic context (IGC) Biological aspect of ancestor (IBA) / Rapid divergence (IRD) Reviewed computational analysis (RCA) / Electronic annotation (IEA) No biological data (ND) / Not annotated or not in background (NA)
species	(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.
background	(vector) gene list to use as background for the enrichment analysis. Default: NA
verbose	(logical) TRUE (default) shows function messages

Details

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

Value

The enrichment results as provided by gprofiler

Examples

## Not run: 
# 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))

## End(Not run)

kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.