gprofiler: Annotate gene list functionally.

In raivokolde/gProfileR: g:ProfileR

Description

Interface to the g:Profiler web toolkit for finding enrichments in gene lists.

Usage

  gprofiler(query, organism = "hsapiens",
    ordered_query = F, significant = T, exclude_iea = F,
    region_query = F, max_p_value = 1, max_set_size = 0,
    correction_method = "analytical",
    hier_filtering = "none", domain_size = "annotated",
    custom_bg = "", numeric_ns = "")

Arguments

organism	gene list origin.
query	vector of gene IDs or a list of such vectors.
ordered_query	when output gene lists are ranked one can use this option to get GSEA style p-values.
significant	whether all or only statistically significant results should be returned.
exclude_iea	exclude electronic annotations (IEA).
region_query	interpret query as chromosomal ranges.
max_p_value	custom p-value threshold, results with a larger p-value are excluded.
max_set_size	maximum size of functional category, larger categories 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.

Value

Data frame with the enrichment analysis results. If the input consisted of several lists the corresponding list is indicated with a variable 'query number'.

Author(s)

Juri Reimand <[e-mail]>, Raivo Kolde <[e-mail]>, Tambet Arak <[e-mail]>

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")

raivokolde/gProfileR documentation built on May 26, 2019, 9:57 p.m.