Commit 483350b2 authored by liiskolb's avatar liiskolb
Browse files

updates catch-up

parent 0b878e6f
......@@ -15,7 +15,7 @@ BugReports: https://biit.cs.ut.ee/gprofiler/page/contact
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
RoxygenNote: 7.1.1
Imports: jsonlite, RCurl, ggplot2, plotly, tidyr (>= 1.0.0), crosstalk, grDevices, gridExtra, grid, viridisLite, dplyr
Depends: R (>= 3.5)
Suggests:
......
......@@ -59,7 +59,7 @@ gp_globals$base_url = "http://biit.cs.ut.ee/gprofiler"
#' @param as_short_link indicator to return results as short-link to the g:Profiler web tool. If set to TRUE, then the function returns the results URL as a character string instead of the data.frame.
#' @return A named list where 'result' contains data.frame with the enrichment analysis results and 'meta' contains metadata needed for Manhattan plot. If the input
#' consisted of several lists the corresponding list is indicated with a variable
#' 'query'.
#' 'query'. The 'result' data.frame is ordered first by the query name, data source (such as GO:BP, GO:CC, GO:MF, REAC, etc), and then by the adjusted p-value.
#' When requesting a 'multi_query', either TRUE or FALSE, the columns of the resulting data frame differ.
#' If 'evcodes' is set, the return value includes columns 'evidence_codes' and 'intersection'.
#' The latter conveys info about the intersecting genes between the corresponding query and term.
......@@ -1114,7 +1114,11 @@ gconvert = function(
# filter empty results
if (filter_na){
df <- df[df$converted != "None",]
df <- df[!df$converted %in% c("nan", "None"),]
}else{
# convert to NA-s
df[df == "nan"] <- NA_character_
df[df == "None"] <- NA_character_
}
if (nrow(df) == 0){
message("No results to show\n", "Please make sure that the organism or namespace is correct")
......
......@@ -14,7 +14,7 @@ gconvert(
)
}
\arguments{
\item{query}{vector that can consist of mixed types of gene IDs (proteins, transcripts, microarray IDs, etc), SNP IDs, chromosomal intervals or term IDs.}
\item{query}{character vector that can consist of mixed types of gene IDs (proteins, transcripts, microarray IDs, etc), SNP IDs, chromosomal intervals or term IDs.}
\item{organism}{organism name. Organism names are constructed by
concatenating the first letter of the name and the family name. Example: human
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/gprofiler2.R
\name{get_version_info}
\alias{get_version_info}
\title{Get version info of g:Profiler data sources}
\usage{
get_version_info(organism = "hsapiens")
}
\arguments{
\item{organism}{organism name. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'.}
}
\value{
A named nested list that includes the versions for all the data sources (GO, KEGG, Reactome, WP, etc) at the time of the data extraction for the given organism.
The versions correspond to the g:Profiler version embedded in the base_url which is also returned by this function under the name 'gprofiler_version'.
}
\description{
Get version info of g:Profiler data sources
}
\examples{
\dontrun{version_info <- get_version_info(organism = "hsapiens")}
}
\author{
Liis Kolberg <liis.kolberg@ut.ee>
}
......@@ -14,7 +14,7 @@ gorth(
)
}
\arguments{
\item{query}{vector of gene IDs to be translated.}
\item{query}{character vector of gene IDs to be translated.}
\item{source_organism}{name of the source organism. Organism names are constructed by concatenating
the first letter of the name and the family name. Example: human - 'hsapiens',
......
......@@ -24,7 +24,7 @@ gost(
)
}
\arguments{
\item{query}{vector, or a (named) list of vectors for multiple queries, that can consist of mixed types of gene IDs (proteins, transcripts, microarray IDs, etc), SNP IDs, chromosomal intervals or term IDs.}
\item{query}{character vector, or a (named) list of character vectors for multiple queries, that can consist of mixed types of gene IDs (proteins, transcripts, microarray IDs, etc), SNP IDs, chromosomal intervals or term IDs.}
\item{organism}{organism name. Organism names are constructed by concatenating the first letter of the name and the
family name. Example: human - 'hsapiens', mouse - 'mmusculus'.}
......@@ -33,8 +33,8 @@ family name. Example: human - 'hsapiens', mouse - 'mmusculus'.}
used to get GSEA style p-values.}
\item{multi_query}{in case of multiple gene lists, returns comparison table of these lists.
If enabled, the result data frame has columns named 'p_values', 'query_sizes', 'intersection_sizes' with vectors showing values in the order of input queries.
Set 'multi_query' to FALSE and simply input query as list of multiple gene vectors to get the results in a long format.}
If enabled, the result data frame has columns named 'p_values', 'gconvert_sizes', 'intersection_sizes' with vectors showing values in the order of input queries.
Set 'multi_gconvert' to FALSE and simply input query as list of multiple gene vectors to get the results in a long format.}
\item{significant}{whether all or only statistically significant results should
be returned.}
......@@ -68,14 +68,14 @@ list and details on incorporated data sources.}
\value{
A named list where 'result' contains data.frame with the enrichment analysis results and 'meta' contains metadata needed for Manhattan plot. If the input
consisted of several lists the corresponding list is indicated with a variable
'query'.
'query'. The 'result' data.frame is ordered first by the query name, data source (such as GO:BP, GO:CC, GO:MF, REAC, etc), and then by the adjusted p-value.
When requesting a 'multi_query', either TRUE or FALSE, the columns of the resulting data frame differ.
If 'evcodes' is set, the return value includes columns 'evidence_codes' and 'intersection'.
The latter conveys info about the intersecting genes between the corresponding query and term.
The result fields are further described in the \href{https://cran.r-project.org/package=gprofiler2/vignettes/gprofiler2.html}{vignette}.
If 'as_short_link' is set to TRUE, then the result is a character short-link to see and share corresponding results via the g:Profiler web tool.
If 'as_short_link' is set to TRUE, then the result is a character short-link to see and share corresponding results via the g:Profiler web tool. In this case, the input gene lists will be stored in a database.
}
\description{
Interface to the g:Profiler tool g:GOSt (\url{https://biit.cs.ut.ee/gprofiler/gost}) for functional enrichments analysis of gene lists.
......@@ -83,6 +83,9 @@ In case the input 'query' is a list of gene vectors, results for multiple querie
If 'multi_query' is selected, the result is a data frame for comparing multiple input lists,
just as in the web tool.
}
\details{
The input gene lists are not stored in g:Profiler unless the option 'as_short_link' is set to TRUE.
}
\examples{
gostres <- gost(c("X:1000:1000000", "rs17396340", "GO:0005005", "ENSG00000156103", "NLRP1"))
......
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