Description Usage Arguments Value Author(s) References Examples
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.
1 2 3 4 5 6 7 | gprofiler(query, organism = "hsapiens", sort_by_structure = T,
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)
|
query |
vector of gene IDs or a list of such vectors. In the latter case,
the query is directed to g:Cocoa, which yields a different graphical output
if requested with the |
organism |
organism name. |
sort_by_structure |
whether hierarchical sorting is enabled or disabled. |
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. |
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).
Juri Reimand <jyri.reimand@ut.ee>, Raivo Kolde <rkolde@gmail.com>, Tambet Arak <tambet.arak@gmail.com>
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
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