@@ -5,19 +5,20 @@

 \alias{pathwaysGMT}

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

 \format{

-a named list of 8080 vectors

+a named list of 1437 vectors

 }

 \usage{

 pathwaysGMT

 }

 \description{

 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}

+\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")

-

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

+    package = "FEDUP")

 Script to prepare data

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

 }

@@ -21,11 +21,11 @@ plotDotPlot(

 \arguments{

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

-\item{x_var}{(char) x-axis variable (must be a column value in `df`).}

+\item{x_var}{(char) x-axis variable (must be a column value in \code{df}).}

-\item{y_var}{(char) y-axis variable (must be a column value in `df`).}

+\item{y_var}{(char) y-axis variable (must be a column value in \code{df}).}

-\item{x_lab}{(char) x-axis label (default `x_var` value).}

+\item{x_lab}{(char) x-axis label (default \code{x_var} value).}

 \item{y_lab}{(char) y-axis label (default NULL).}

@@ -35,11 +35,11 @@ plotDotPlot(

 \item{fill_col}{(char) point fill colours (default NULL).}

-\item{fill_lab}{(char) point fill label (default `fill_var` value).}

+\item{fill_lab}{(char) point fill label (default \code{fill_var} value).}

 \item{size_var}{(char) point size variable (default NULL).}

-\item{size_lab}{(char) point size label (default `size_var` value).}

+\item{size_lab}{(char) point size label (default \code{size_var} value).}

 }

 \value{

 object returned from ggplot with the enrichment dot plot.

@@ -56,12 +56,12 @@ fedup_plot <- fedup_res[which(fedup_res$qvalue < 0.05),]

 fedup_plot$log10qvalue <- -log10(fedup_plot$qvalue + 1e-10)

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

 plotDotPlot(

-     df = fedup_plot,

-     x_var = "log10qvalue",

-     y_var = "pathway",

-     x_lab = "-log10(Qvalue)",

-     fill_var = "enrichment",

-     fill_lab = "Enrichment\nstatus",

-     size_var = "real_pathway_frac",

-     size_lab = "Gene fraction")

+    df = fedup_plot,

+    x_var = "log10qvalue",

+    y_var = "pathway",

+    x_lab = "-log10(Qvalue)",

+    fill_var = "status",

+    fill_lab = "Enrichment\nstatus",

+    size_var = "fold_enrichment",

+    size_lab = "Fold enrichment")

 }

@@ -41,20 +41,20 @@ pathways using EnrichmentMap (EM) in Cytoscape.

 }

 \examples{

 \dontrun{

- # not run because Cytoscape needs to be installed and open

- data(testGene)

- data(backgroundGene)

- data(pathwaysGMT)

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

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

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

- net_file <- tempfile("FEDUP_EM", fileext = ".png")

- writePathways(pathwaysGMT, gmt_file)

- writeFemap(fedup_res, results_file)

- plotFemap(

-   gmt_file = gmt_file,

-   results_file = results_file,

-   qvalue = 0.05,

-   net_name = "FEDUP_EM",

-   net_file = net_file)}

+    # not run because Cytoscape needs to be installed and open

+    data(testGene)

+    data(backgroundGene)

+    data(pathwaysGMT)

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

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

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

+    net_file <- tempfile("FEDUP_EM", fileext = ".png")

+    writePathways(pathwaysGMT, gmt_file)

+    writeFemap(fedup_res, results_file)

+    plotFemap(

+        gmt_file = gmt_file,

+        results_file = results_file,

+        qvalue = 0.05,

+        net_name = "FEDUP_EM",

+        net_file = net_file)}

 }

@@ -7,7 +7,7 @@ Currently supports the following file format: GMT, TXT, XLSX.}

 \usage{

 readPathways(

   pathway_file,

-  header = TRUE,

+  header = FALSE,

   pathway_col = NULL,

   gene_col = NULL,

   MIN_GENE = 1L,

@@ -18,13 +18,14 @@ readPathways(

 \arguments{

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

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

+\item{header}{(logical) whether \code{pathway_file} has a header

+(default FALSE).}

 \item{pathway_col}{(char) column name with pathway identifiers.

-For use with for non-GMT input files (eg "Pathway.ID"; default NULL).}

+For use with non-GMT input files (eg "Pathway.ID"; default NULL).}

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

-For use with for non-GMT input files (eg "Gene.ID"; default NULL).}

+For use with non-GMT input files (eg "Gene.ID"; default NULL).}

 \item{MIN_GENE}{(integer) minimum number of genes to be considered

 in a pathway (default = 1).}

@@ -32,8 +33,8 @@ 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 (BP, MF and/or CC, default NULL).}

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

+which class(es) should be subsetted (BP, MF and/or CC, default NULL).}

 }

 \value{

 a list of vectors with pathway annotations.

@@ -44,10 +45,9 @@ 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)

+    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)

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

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

 }

@@ -7,7 +7,7 @@

 runFedup(test_gene, background_gene, pathways)

 }

 \arguments{

-\item{test_gene}{(char) vector of genes to test set.}

+\item{test_gene}{(char) vector of genes to use as test set.}

 \item{background_gene}{(char) vector of genes to use as background set.}

@@ -17,21 +17,20 @@ runFedup(test_gene, background_gene, pathways)

 table of pathway enrichment and depletion results. Rows represent

 tested pathways. Columns represent:

 \itemize{

- \item pathway -- name of the pathway, corresponds to names(pathways);

- \item size -- size of the pathway;

- \item real_total -- number of genes in `test_gene`;

- \item real_pathway -- number of `test_gene` members in pathway;

- \item real_pathway_frac -- fraction of `test_gene` members in pathway,

-     evaluates as (`real_pathawy` / `real_total`) * 100;

- \item expected_total -- number of genes in 'background_gene';

- \item expected_pathway -- number of `background_gene` members in pathway;

- \item expected_pathway_frac -- fraction of `background_gene` members in

-     pathway, evaluates as (`expected_pathway` / `expected_total`) * 100;

- \item enrichment -- indicator that pathway is enriched or depleted for

-     `test_gene` members;

- \item real_pathway_gene -- vector of `real_pathway` genes;

- \item pvalue -- enrichment p-value calculated via Fisher's exact test;

- \item qvalue -- BH-adjusted p-value

+    \item pathway -- name of the pathway, corresponds to

+        names(\code{pathways});

+    \item size -- size of the pathway;

+    \item real_frac -- fraction of \code{test_gene} members in pathway;

+    \item expected_frac -- fraction of \code{background_gene} members in

+        pathway;

+    \item fold_enrichment -- fold enrichment measure,

+        evaluates as \code{real_frac} / \code{expected_frac};

+    \item status -- indicator that pathway is enriched or depleted for

+        \code{test_gene} members;

+    \item real_gene -- vector of \code{test_gene} gene members annotated

+        to \code{pathways};

+    \item pvalue -- enrichment p-value calculated via Fisher's exact test;

+    \item qvalue -- BH-adjusted p-value

 }

 }

 \description{

@@ -5,7 +5,7 @@

 \alias{testGene}

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

 \format{

-a character vector with 396 elements (gene IDs)

+a character vector with 190 elements (gene IDs)

 }

 \usage{

 testGene

@@ -16,13 +16,14 @@ writeFemap(df, results_file)

 table of gene enrichment and depletion results formatted as a

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

 \itemize{

-   \item pathway -- pathway ID (must match pathway IDs in the GMT file provided to plotFemap());

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

-   \item pvalue -- enrichment pvalue;

-   \item qvalue -- BH-corrected pvalue;

-   \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)

+    \item pathway -- pathway ID (must match pathway IDs in the GMT file

+        provided to plotFemap());

+    \item description -- pathway name or description;

+    \item pvalue -- enrichment pvalue;

+    \item qvalue -- BH-corrected pvalue;

+    \item status -- +1 or -1, to identify enrichment in either of the two

+        phenotypes being compared in the two-class analysis

+        (+1 maps to red, -1 maps to blue)

 }

 }

 \description{

@@ -14,9 +14,9 @@ writePathways(pathways, gmt_file)

 \value{

 GMT-formatted file. Rows represent pathways. Columns represent:

 \itemize{

- \item pathway ID;

- \item description;

- \item a list of tab-delimited genes

+    \item pathway ID;

+    \item description;

+    \item a list of tab-delimited genes

 }

 }

 \description{