Commit 22a16adc authored by liiskolb's avatar liiskolb
Browse files

change IEA default value

parent 57a2ca80
......@@ -67,7 +67,7 @@ gost <- function(query,
ordered_query = FALSE,
multi_query = FALSE,
significant = TRUE,
exclude_iea = TRUE,
exclude_iea = FALSE,
measure_underrepresentation = FALSE,
evcodes = FALSE,
user_threshold = 0.05,
......
......@@ -5,7 +5,7 @@
\title{Gene list functional enrichment.}
\usage{
gost(query, organism = "hsapiens", ordered_query = FALSE,
multi_query = FALSE, significant = TRUE, exclude_iea = TRUE,
multi_query = FALSE, significant = TRUE, exclude_iea = FALSE,
measure_underrepresentation = FALSE, evcodes = FALSE,
user_threshold = 0.05, correction_method = c("g_SCS", "bonferroni",
"fdr", "false_discovery_rate", "gSCS", "analytical"),
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/gprofiler2.R
\name{publish_gosttable}
\alias{publish_gosttable}
\title{Create and save a table with the functional enrichment analysis results.}
\usage{
publish_gosttable(gostres, highlight_terms = NULL, use_colors = TRUE,
show_columns = c("source", "term_name", "term_size",
"intersection_size"), filename = NULL)
}
\arguments{
\item{gostres}{named list from gost() function (with names 'result' and 'meta') or a data frame that has columns named "term_id" and "p_value(s)".}
\item{highlight_terms}{vector of selected term IDs from the analysis or a (subset) data.frame that has a column called 'term_id'. All data is shown if set to NULL.}
\item{use_colors}{if enabled, the p-values are highlighted in the viridis colorscale just as in g:Profiler, otherwise the table has no background colors.}
\item{show_columns}{names of additional columns to show besides term_id and p_value. By default the output table shows additional columns named "source", "term_name", "term_size", "intersection_size"}
\item{filename}{file name to create on disk and save the annotated plot. Filename extension should be from c("png", "pdf", "jpeg", "tiff", "bmp").}
}
\value{
The output is a ggplot object.
}
\description{
This function creates a table mainly for the results from gost() function.
However, if the input at least contains columns named 'term_id' and 'p_value' then any enrichment results data frame can be visualised in a table with this function.
}
\details{
The output table is very similar to the one shown under the Manhattan plot.
}
\examples{
gostres <- gost(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")
publish_gosttable(gostres, highlight_terms = c("GO:0001010", "WP:WP1763"))
}
\author{
Liis Kolberg <liis.kolberg@ut.ee>
}
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment