Package 'gProfileR'

Convert gene IDs.

Description

Interface to the g:Convert tool. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'.

Usage

gconvert(query, organism = "hsapiens", target = "ENSG",
  region_query = F, numeric_ns = "", mthreshold = Inf,
  filter_na = T, df = T)

Arguments

query	list of gene IDs.
organism	organism name.
target	target namespace.
region_query	interpret query as chromosomal ranges.
numeric_ns	namespace to use for fully numeric IDs.
mthreshold	maximum number of results per initial alias to show.
filter_na	logical indicating whether to filter out results without a corresponding target.
df	logical indicating whether the output will be a data.frame or list.

Value

The output can be either a list or a data.frame. The list has an entry for every input gene. The data frame is a table closely corresponding to the web interface output.

Author(s)

Juri Reimand <[email protected]>, Raivo Kolde <[email protected]>, Tambet Arak <[email protected]>

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

## Not run: 
 gconvert(c("POU5F1", "SOX2", "NANOG"), organism = "hsapiens", target="AFFY_HG_U133_PLUS_2")

## End(Not run)

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Get the base URL.

Description

Get the base URL.

Usage

get_base_url()

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Get the TLS version for SSL

Description

Get the TLS version for SSL

Usage

get_tls_version()

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Get current user agent string.

Description

Get the HTTP User-Agent string.

Usage

get_user_agent()

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Find orthologs.

Description

Interface to the g:Orth tool. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'.

Usage

gorth(query, source_organism = "hsapiens",
  target_organism = "mmusculus", region_query = F, numeric_ns = "",
  mthreshold = Inf, filter_na = T, df = T)

Arguments

query	list of gene IDs to be translated.
source_organism	name of the source organism.
target_organism	name of the target organism.
region_query	interpret query as chromosomal ranges.
numeric_ns	namespace to use for fully numeric IDs.
mthreshold	maximum number of ortholog names per gene to show.
filter_na	logical indicating whether to filter out results without a corresponding target name.
df	logical indicating whether the output will be a data.frame or list.

Details

To alleviate the problem of having many orthologs per gene (most of them uninformative) one can set a threshold for the number of results. The program tries to find the most informative by selecting the most popular ones.

Value

The output can be either a list or a data.frame. The list has an entry for every input gene. The data frame is a table closely corresponding to the web interface output.

Author(s)

Raivo Kolde <[email protected]>, Juri Reimand <[email protected]>, Tambet Arak <[email protected]>

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

## Not run: 
 gorth(c("Klf4","Pax5","Sox2","Nanog"), source_organism="mmusculus", target_organism="hsapiens")

## End(Not run)

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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", 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)

Arguments

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 png_fn parameter.
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.

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 <[email protected]>, Raivo Kolde <[email protected]>, Tambet Arak <[email protected]>

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

## Not run: 
 gprofiler(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")

## End(Not run)

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Set the base URL.

Description

Set the base URL. Useful for overriding the default URL (http://biit.cs.ut.ee/gprofiler) with the bleeding-edge beta or an archived version.

Usage

set_base_url(url)

Arguments

url	the base URL.

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Set the TLS version to use for SSL

Description

Set the TLS version. Could be useful at environments where SSL was built without TLS 1.2 support

Usage

set_tls_version(v)

Arguments

v	version: "1.2" (default), "1.1" (fallback)

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Set custom user agent string.

Description

Set the HTTP User-Agent string. Useful for overriding the default user agent for packages that depend on gProfileR functionality.

Usage

set_user_agent(ua, append = F)

Arguments

ua	the user agent string.
append	logical indicating whether to append the passed string to the default user agent string.

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