Commit caf1af81 authored by domingue's avatar domingue
Browse files

Updated manual pages

parent a4273b4d
Pipeline #1836 failed with stage
in 31 minutes and 56 seconds
......@@ -50,6 +50,7 @@ export(pick)
export(plotPDF)
export(plot_ci)
export(pp)
export(prettify)
export(pretty_columns)
export(pretty_names)
export(print_all)
......@@ -84,6 +85,7 @@ import(ggplot2)
importFrom(BiocManager,available)
importFrom(BiocManager,install)
importFrom(DT,datatable)
importFrom(RColorBrewer,brewer.pal)
importFrom(ReactomePA,enrichPathway)
importFrom(assertthat,assert_that)
importFrom(biomaRt,getBM)
......
......@@ -24,6 +24,8 @@ A convenient wrapper for clusterProfiler enrichment. I will attempt to do all th
}
\examples{
\dontrun{
entrez <- c("20832", "27061", "22335", "12343", "66997", "98238", "13682", "22145", "18000", "595136", "19943", "12751", "11737", "68021", "22195", "105245")
cp_test(entrez, annoDb = "org.Mm.eg.db", cp_species = "mouse")
}
}
......@@ -19,6 +19,6 @@ Create a custom color palette for a fixed set of values
}
\examples{
\dontrun{
create_palette(c(letters[1:3]))
}
}
......@@ -21,8 +21,3 @@ a vector of gene IDs
\description{
Extract hits from the table of DGE. Assumes the output format from the corescf DGE workflow.
}
\examples{
\dontrun{
}
}
......@@ -20,8 +20,3 @@ Wrapper for \code{\link[cummeRbund:repFpkmMatrix]{cummeRbund::repFpkmMatrix()}}
\note{
cummeRbund is now very old and has been superseded by better tools. It should not be the first choice for gene expression analysis.
}
\examples{
\dontrun{
}
}
......@@ -12,8 +12,3 @@ Deprecated. Since it assumes that the default ensembl is used which is never a g
\note{
It's not even working because \code{filter(biomart == "ensembl")} returns nothing.
}
\examples{
\dontrun{
}
}
......@@ -16,8 +16,3 @@ retainExprGenes(df, id_col = "ensembl_gene_id", ...)
\description{
#' Deprecated, use \code{\link[corescf:filter_expressed_genes]{corescf::filter_expressed_genes()}} instead.
}
\examples{
\dontrun{
}
}
......@@ -19,8 +19,3 @@ a data.frame
\description{
Subset genes that are significantly differentially expressed
}
\examples{
\dontrun{
}
}
......@@ -24,8 +24,3 @@ Subset a list of non-differentially expressed genes
\note{
Doesn't seem to be have been used for a long time.
}
\examples{
\dontrun{
}
}
......@@ -19,8 +19,3 @@ a data.frame
\description{
Subset genes that are significantly higher expressed in sample1 compared to sample2
}
\examples{
\dontrun{
}
}
......@@ -19,8 +19,3 @@ a data.frame
\description{
Subset genes that are significantly less expressed in sample1 compared to sample2
}
\examples{
\dontrun{
}
}
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