R: Annotate gene list functionally.

gprofiler {gProfileR} | R Documentation

## Annotate gene list functionally.

### Description

Interface to the g:Profiler tool for finding enrichments in gene lists. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'. If requesting PNG output, the request is directed to the g:GOSt tool in case 'query' is a vector and the g:Cocoa (compact view of multiple queries) tool in case 'query' is a list. PNG output can fail (return FALSE) in case the input query is too large. In such case, it is advisable to fall back to a non-image request.

### Usage

    gprofiler(query, organism = "hsapiens", ordered_query = F,
      significant = T, exclude_iea = F, underrep = F, evcodes = F,
      region_query = F, max_p_value = 1, min_set_size = 0, max_set_size = 0,
      min_isect_size = 0, correction_method = "analytical",
      hier_filtering = "none", domain_size = "annotated", custom_bg = "",
      numeric_ns = "", png_fn = NULL, include_graph = F, src_filter = NULL)

### Arguments

`query` | vector of gene IDs or a list of such vectors.
`organism` | organism name.
`ordered_query` | in case output gene lists are ranked this option may be used to get GSEA style p-values.
`significant` | whether all or only statistically significant results should be returned.
`exclude_iea` | exclude electronic annotations (IEA).
`underrep` | measure underrepresentation.
`evcodes` | include GO evidence codes as the final column of output. Note that this can decrease performance and make the query slower.
`region_query` | interpret query as chromosomal ranges.
`max_p_value` | custom p-value threshold, results with a larger p-value are excluded.
`min_set_size` | minimum size of functional category, smaller categories are excluded.
`max_set_size` | maximum size of functional category, larger categories are excluded.
`min_isect_size` | minimum size of the overlap (intersection) between query and functional category, smaller intersections are excluded.
`correction_method` | the algorithm used for determining the significance threshold, one of "gSCS", "fdr", "bonferroni".
`hier_filtering` | hierarchical filtering strength, one of "none", "moderate", "strong".
`domain_size` | statistical domain size, one of "annotated", "known".
`custom_bg` | vector of gene names to use as a statistical background.
`numeric_ns` | namespace to use for fully numeric IDs.
`png_fn` | request the result as PNG image and write it to png_fn.
`include_graph` | request inclusion of network data with the result.
`src_filter` | a vector of data sources to use. Currently, these include GO (GO:BP, GO:MF, GO:CC to select a particular GO branch), KEGG, REAC, TF, MI, CORUM, HP, HPA, OMIM. Please see the g:GOSt web tool for the comprehensive list and details on incorporated data sources.

### Value

A data frame with the enrichment analysis results. If the input consisted of several lists the corresponding list is indicated with a variable 'query number'. When requesting a PNG image, either TRUE or FALSE, depending on whether a non-empty result was received and a file written or not, respectively. If 'include_graph' is set, the return value may include the attribute 'networks', containing a list of all network sources, each in turn containing a list of graph edges. The edge structure is a list containing the two interacting symbols and two boolean values (in that order), indicating whether the first or second interactor is part of the input query (core nodes).

### Author(s)

Juri Reimand <jyri.reimand@ut.ee>, Raivo Kolde <rkolde@gmail.com>, Tambet Arak <tambet.arak@gmail.com>

### References

J. Reimand, M. Kull, H. Peterson, J. Hansen, J. Vilo: g:Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments (2007) NAR 35 W193-W200

### Examples

     gprofiler(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")

[Package gProfileR version 0.6.1 Index]