@@ -1,13 +1,17 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/fedup-data.R

+% Please edit documentation in R/data.R

 \docType{data}

 \name{backgroundGene}

 \alias{backgroundGene}

-\title{Example vector of human genes to use as background set for enrichment.

-Script to generate example background gene vector

-system.file("genes.R", package = "FEDUP")}

+\title{Example vector of human genes to use as background set for enrichment.}

+\format{

+a character vector with 15965 elements (gene IDs)

+}

+\usage{

+backgroundGene

+}

 \description{

-Example vector of human genes to use as background set for enrichment.

-Script to generate example background gene vector

-system.file("genes.R", package = "FEDUP")

+Script to generate data

+system.file("data-raw", "genes.R", package = "FEDUP")

 }

+\keyword{datasets}

@@ -1,13 +1,24 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/fedup-data.R

+% Please edit documentation in R/data.R

 \docType{data}

 \name{pathwaysGMT}

 \alias{pathwaysGMT}

-\title{Example list of human pathway annotations obtained from a GMT file.

-Script to generate example pathway list

-system.file("pathwaysGMT.R", package = "FEDUP")}

+\title{Named list of human pathway annotations obtained from a GMT file.}

+\format{

+a named list of 8080 vectors

+}

+\usage{

+pathwaysGMT

+}

 \description{

-Example list of human pathway annotations obtained from a GMT file.

-Script to generate example pathway list

-system.file("pathwaysGMT.R", package = "FEDUP")

+Raw GMT file is available from

+\url{http://download.baderlab.org/EM_Genesets/November_17_2020/Human/symbol/Pathways/Human_Reactome_November_17_2020_symbol.gmt}

+}

+\details{

+Raw data location

+system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt", package = "FEDUP")

+

+Script to prepare data

+system.file("data-raw", "pathwaysGMT.R", package = "FEDUP")

 }

+\keyword{datasets}

@@ -1,13 +1,21 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/fedup-data.R

+% Please edit documentation in R/data.R

 \docType{data}

 \name{pathwaysXLSX}

 \alias{pathwaysXLSX}

-\title{Example list of yeast SAFE terms obtained from a XLSX file.

-Script to generate example pathway list

-system.file("pathwaysXLSX.R", package = "FEDUP")}

+\title{Example list of yeast SAFE terms obtained from a XLSX file.}

+\format{

+a named list of 30 vectors

+}

+\usage{

+pathwaysXLSX

+}

 \description{

-Example list of yeast SAFE terms obtained from a XLSX file.

-Script to generate example pathway list

-system.file("pathwaysXLSX.R", package = "FEDUP")

+Raw data location

+system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP")

+}

+\details{

+Script to prepare data

+system.file("data-raw", "pathwaysXLSX.R", package = "FEDUP")

 }

+\keyword{datasets}

@@ -52,20 +52,17 @@ data(testGene)

 data(backgroundGene)

 data(pathwaysGMT)

 fedup_res <- runFedup(testGene, backgroundGene, pathwaysGMT)

-fedup_res$log10fdr <- -log10(fedup_res$fdr) # log10-transform FDR for plotting

-fedup_enr <- head(fedup_res[with(fedup_res, which(enrichment == "enriched")),], 10)

-fedup_dep <- head(fedup_res[with(fedup_res, which(enrichment == "depleted")),], 10)

-fedup_plot <- rbind(fedup_enr, fedup_dep)

+fedup_plot <- fedup_res[which(fedup_res$fdr < 0.05),]

 fedup_plot$log10fdr <- -log10(fedup_plot$fdr + 1e-10) # log10-transform FDR for plotting

 fedup_plot$pathway <- gsub("\\\\\%.*", "", fedup_plot$pathway) # clean pathway names

-\dontrun{

-plotDotPlot(df = fedup_plot,

-            x_var = "log10fdr",

-            y_var = "pathway",

-            x_lab = "-log10(FDR)",

-            fill_var = "enrichment",

-            fill_lab = "Enrichment",

-            size_var = "real_pathway_frac",

-            size_lab = "Gene fraction")

-}

+ plotDotPlot(

+    df = fedup_plot,

+    x_var = "log10fdr",

+    y_var = "pathway",

+    x_lab = "-log10(FDR)",

+    fill_var = "enrichment",

+    fill_lab = "Enrichment",

+    size_var = "real_pathway_frac",

+    size_lab = "Gene fraction"

+ )

 }

@@ -2,40 +2,47 @@

 % Please edit documentation in R/femap.R

 \name{plotFemap}

 \alias{plotFemap}

-\title{Plots an EnrichmentMap in Cytoscape to visualize enriched gene sets}

+\title{Plots an EnrichmentMap (EM) in Cytoscape to visualize enriched and depleted gene sets.}

 \usage{

-plotFemap(

-  gmt_file,

-  EM_file,

-  EM_group_file,

-  output_folder,

-  net_name = "generic",

-  image_format = "png"

-)

+plotFemap(gmt_file, results_file, pvalue = 1, qvalue = 1, net_name = "generic")

 }

 \arguments{

-\item{gmt_file}{(char) file path to GMT file (this needs to be absolute path name).}

-

-\item{EM_file}{(char) file path to results_EM.txt (generated by writeEmapFile.R).}

-

-\item{EM_group_file}{(char) file path to write pathway groupings as determined

-by EnrichmentMap.}

+\item{gmt_file}{(char) path to GMT file (must be absolute path)}

-\item{output_folder}{(char) file path to write gene set grouping file. This will be

-used for between-pathway SNP association analysis.}

+\item{results_file}{(char) path to file with enrichment results (must be absolute path)}

-\item{net_name}{(char) name for network in Cytoscape.}

+\item{pvalue}{(numeric) pvalue cutoff (value between 0 and 1). Gene set

+nodes with a p-value lower than the given value will not be included

+   in the network. (default = 1)}

-\item{image_format}{(char) one of PNG, PDF, SVG, or JPEG.

+\item{qvalue}{(numeric) FDR qvalue cutoff (value between 0 and 1). Gene set

+nodes with a p-value lower than the given value will not be included

+in the network. (default = 1)}

-# Not run because requires Cytoscape to be installed and open.

-# plotEmap(gmt_file=gmt_file, EM_file=EM_file, output_folder=enrich_folder,

-    net_name="generic", image_format="png").}

+\item{net_name}{(char) name for network in Cytoscape}

 }

 \value{

-Filename of image to which EnrichmentMap is exported. Also side

-		effect of plotting the EnrichmentMap in an open session of Cytoscape.

+filename of image to which EM is exported. Also side effect of

+ plotting the EM in an open session of Cytoscape.

 }

 \description{

-Plots an EnrichmentMap in Cytoscape to visualize enriched gene sets

+Plots an EnrichmentMap (EM) in Cytoscape to visualize enriched and depleted gene sets.

+}

+\examples{

+\dontrun{

+# not run because this function requires Cytoscape to be installed and open

+data(testGene)

+data(backgroundGene)

+data(pathwaysGMT)

+gmt_file <- tempfile("pathwaysGMT", fileext = ".gmt")

+writePathways(pathwaysGMT, gmt_file)

+fedup_res <- runFedup(testGene, backgroundGene, pathwaysGMT)

+results_file <- tempfile("fedup_res", fileext = ".txt")

+writeFemap(fedup_res, results_file)

+plotFemap(

+	gmt_file = gmt_file,

+	results_file = results_file,

+	qvalue = 0.05,

+	net_name = "FEDUP_EM"

+)}

 }

new file mode 100644

@@ -0,0 +1,56 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/pathways.R

+\name{readPathways}

+\alias{readPathways}

+\title{Returns a list of pathways from a variety of file formats.

+Currently supports the following file format: GMT, TXT, XLSX}

+\usage{

+readPathways(

+  pathway_file,

+  header = TRUE,

+  pathway_col,

+  gene_col,

+  MIN_GENE = 1L,

+  MAX_GENE = Inf,

+  GO_class = NULL

+)

+}

+\arguments{

+\item{pathway_file}{(char) path to file with pathway annotations}

+

+\item{header}{(logical) whether pathway_file has a header (default = TRUE)}

+

+\item{pathway_col}{(char) column name with pathway identifiers, one pathway per row

+use for non-GMT input (eg "Pathway.ID", default = NULL)}

+

+\item{gene_col}{(char) column name with gene identifiers

+use for non-GMT input (eg "Gene.ID", default = NULL)}

+

+\item{MIN_GENE}{(integer) minimum number of genes to be considered in a pathway

+(default = 1)}

+

+\item{MAX_GENE}{(integer) maximum number of genes to be considered in a pathway

+(default = Inf)}

+

+\item{GO_class}{(char) if GO terms are present in 'pathway_file', which

+class(es) should be subsetted (i.e., BP, MF, CC)

+(default = NULL)}

+}

+\value{

+a list of vectors with pathway annotations

+}

+\description{

+Returns a list of pathways from a variety of file formats.

+Currently supports the following file format: GMT, TXT, XLSX

+}

+\examples{

+pathways <- readPathways(

+ system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",

+ package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500

+)

+pathways <- readPathways(

+ system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),

+ header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID",

+ MIN_GENE = 10, MAX_GENE = 500

+)

+}

@@ -1,13 +1,17 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/fedup-data.R

+% Please edit documentation in R/data.R

 \docType{data}

 \name{testGene}

 \alias{testGene}

-\title{Example vector of human genes to use as test set for enrichment.

-Script to generate example test gene vector

-system.file("genes.R", package = "FEDUP")}

+\title{Example vector of human genes to use as test set for enrichment.}

+\format{

+a character vector with 396 elements (gene IDs)

+}

+\usage{

+testGene

+}

 \description{

-Example vector of human genes to use as test set for enrichment.

-Script to generate example test gene vector

-system.file("genes.R", package = "FEDUP")

+Script to prepare data

+system.file("data-raw", "genes.R", package = "FEDUP")

 }

+\keyword{datasets}

new file mode 100644

@@ -0,0 +1,38 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/femap.R

+\name{writeFemap}

+\alias{writeFemap}

+\title{Writes an enrichment dataset file for use in Cytoscape EnrichmentMap}

+\usage{

+writeFemap(df, results_file)

+}

+\arguments{

+\item{df}{(data.frame) table with FEDUP enrichment results

+(see ?runFedup() for column descriptions)}

+

+\item{results_file}{(char) name of output results file}

+}

+\value{

+table of gene enrichment and depletion results formatted as a

+'Generic results file'. Rows represent tested pathways. Columns represent:

+\itemize{

+   \item geneset -- gene-set ID (must match the gene-set ID in the GMT file);

+   \item description -- gene-set name or description;

+   \item pvalue -- enrichment pvalue;

+   \item qvalue -- FDR correction value;

+   \item phenotype -- +1 or -1, to identify enrichment in up- and down-regulation,

+            or, more in general in either of the two phenotypes being compared

+            in the two-class analysis (+1 maps to red, -1 maps to blue)

+}

+}

+\description{

+Writes an enrichment dataset file for use in Cytoscape EnrichmentMap

+}

+\examples{

+data(testGene)

+data(backgroundGene)

+data(pathwaysGMT)

+fedup_res <- runFedup(testGene, backgroundGene, pathwaysGMT)

+results_file <- tempfile("fedup_res", fileext = ".txt")

+writeFemap(fedup_res, results_file)

+}

@@ -2,54 +2,27 @@

 % Please edit documentation in R/pathways.R

 \name{writePathways}

 \alias{writePathways}

-\title{Returns a list of pathways from a file.

-Currently supports the following file format: GMT, TXT, XLSX}

+\title{Writes a set of pathways (list of vectors) to a GMT file}

 \usage{

-writePathways(

-  pathway_file,

-  header = TRUE,

-  pathway_col,

-  gene_col,

-  MIN_GENE = 1L,

-  MAX_GENE = Inf,

-  GO_class = NULL

-)

+writePathways(pathways, gmt_file)

 }

 \arguments{

-\item{pathway_file}{(char) path to file with pathway annotations}

+\item{pathways}{(list) named list of vectors}

-\item{header}{(logical) whether pathway_file has a header (default = TRUE)}

-

-\item{pathway_col}{(char) column name with pathway identifiers, one pathway per row

-use for non-GMT input (eg "Pathway.ID", default = NULL)}

-

-\item{gene_col}{(char) column name with gene identifiers

-use for non-GMT input (eg "Gene.ID", default = NULL)}

-

-\item{MIN_GENE}{(integer) minimum number of genes to be considered in a pathway

-(default = 1)}

-

-\item{MAX_GENE}{(integer) maximum number of genes to be considered in a pathway

-(default = Inf)}

-

-\item{GO_class}{(char) if GO terms are present in 'pathway_file', which class(es)

-should be used (i.e., BP, MF, CC) (default = NULL)}

+\item{gmt_file}{(char) name of output GMT file}

 }

 \value{

-a list of vectors with pathway annotations

+GMT formatted file. Rows represent gene sets. Columns represent:

+\itemize{

+   \item gene set name;

+   \item description;

+   \item a list of tab-delimited genes

+}

 }

 \description{

-Returns a list of pathways from a file.

-Currently supports the following file format: GMT, TXT, XLSX

+Writes a set of pathways (list of vectors) to a GMT file

 }

 \examples{

-pathways <- writePathways(

- system.file("extdata", "Human_GOBP_AllPathways_no_GO_iea_November_17_2020_symbol.gmt", package = "FEDUP"),

- MIN_GENE = 10, MAX_GENE = 500,

-)

-pathways <- writePathways(

- system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),

- header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID",

- MIN_GENE = 10, MAX_GENE = 500

-)

+data(pathwaysXLSX)

+writePathways(pathwaysXLSX, tempfile("pathwaysXLSX", fileext = ".gmt"))

 }