markdownified roxygen blocks

R/correlatePCs.R

@@ -2,15 +2,15 @@
 #'
 #' Computes the significance of (cor)relations between PCA scores and the sample
 #' experimental covariates, using Kruskal-Wallis test for categorial variables
-#' and the \code{cor.test} based on Spearman's correlation for continuous
+#' and the `cor.test` based on Spearman's correlation for continuous
 #' variables
 #'
-#' @param pcaobj A \code{prcomp} object
-#' @param coldata A \code{data.frame} object containing the experimental
+#' @param pcaobj A `prcomp` object
+#' @param coldata A `data.frame` object containing the experimental
 #' covariates
 #' @param pcs A numeric vector, containing the corresponding PC number
 #'
-#' @return A \code{data.frame} object with computed p values for each covariate
+#' @return A `data.frame` object with computed p values for each covariate
 #' and for each principal component
 #'
 #' @examples
@@ -53,10 +53,10 @@ correlatePCs <- function(pcaobj, coldata, pcs = 1:4) {
 #'
 #' Plots the significance of the (cor)relation of each covariate vs a principal component
 #'
-#' @param pccorrs A \code{data.frame} object generated by \link{correlatePCs}
+#' @param pccorrs A `data.frame` object generated by [correlatePCs]
 #' @param pc An integer number, corresponding to the principal component of
 #' interest
-#' @param logp Logical, defaults to \code{TRUE}, displays the -\code{log10} of
+#' @param logp Logical, defaults to `TRUE`, displays the -`log10` of
 #' the pvalue instead of the p value itself
 #'
 #' @return A base plot object

R/deprecated.R

@@ -16,7 +16,7 @@
 #' 
 #' @section Transitioning to the mosdef framework:
 #' 
-#' * [topGOtable()] is now being replaced by the more flexible 
+#' - [topGOtable()] is now being replaced by the more flexible 
 #' [mosdef::run_topGO()] function
 #' 
 #' @author Federico Marini

R/distro_expr.R

@@ -1,8 +1,8 @@
 #' Plot distribution of expression values
 #'
-#' @param rld A \code{\link{DESeqTransform}} object.
-#' @param plot_type Character, choose one of \code{boxplot}, \code{violin} or
-#' \code{density}. Defaults to \code{density}
+#' @param rld A [DESeqTransform()] object.
+#' @param plot_type Character, choose one of `boxplot`, `violin` or
+#' `density`. Defaults to `density`
 #'
 #' @return A plot with the distribution of the expression values
 #' @export

R/genespca.R

@@ -3,14 +3,14 @@
 #' Computes and plots the principal components of the genes, eventually displaying
 #' the samples as in a typical biplot visualization.
 #'
-#' The implementation of this function is based on the beautiful \code{ggbiplot}
+#' The implementation of this function is based on the beautiful `ggbiplot`
 #' package developed by Vince Vu, available at https://github.com/vqv/ggbiplot.
 #' The adaptation and additional parameters are tailored to display typical genomics data
 #' such as the transformed counts of RNA-seq experiments
 #'
-#' @param x A \code{\link{DESeqTransform}} object, with data in \code{assay(x)},
-#' produced for example by either \code{\link{rlog}} or
-#' \code{\link{varianceStabilizingTransformation}}
+#' @param x A [DESeqTransform()] object, with data in `assay(x)`,
+#' produced for example by either [rlog()] or
+#' [varianceStabilizingTransformation()]
 #' @param ntop Number of top genes to use for principal components,
 #' selected by highest row variance
 #' @param choices Vector of two numeric values, to select on which principal components to plot
@@ -37,7 +37,7 @@
 #' @param circle.prob Size of the correlation circle in Normal probability
 #' @param varname.size Size of the text for variable names
 #' @param varname.adjust  Adjustment factor the placement of the variable names,
-#'  >= 1 means farther from the arrow
+#' '>= 1' means farther from the arrow
 #' @param varname.abbrev  Logical, whether or not to abbreviate the variable names
 #' @param returnData Logical, if TRUE returns a data.frame for further use, containing the
 #' selected principal components for custom plotting
@@ -47,10 +47,10 @@
 #' to allow for distinguishing where the variables are plotted
 #' @param useRownamesAsLabels Logical, if TRUE uses the row names as labels for plotting
 #' @param point_size Size of the points to be plotted for the observations (genes)
-#' @param annotation A \code{data.frame} object, with row.names as gene identifiers (e.g. ENSEMBL ids)
-#' and a column, \code{gene_name}, containing e.g. HGNC-based gene symbols
+#' @param annotation A `data.frame` object, with row.names as gene identifiers (e.g. ENSEMBL ids)
+#' and a column, `gene_name`, containing e.g. HGNC-based gene symbols
 #'
-#' @return An object created by \code{ggplot}, which can be assigned and further customized.
+#' @return An object created by `ggplot`, which can be assigned and further customized.
 #'
 #' @examples
 #'

R/get_annotation.R

@@ -1,12 +1,12 @@
 #' Get an annotation data frame from biomaRt
 #'
-#' @param dds A \code{\link{DESeqDataSet}} object
+#' @param dds A [DESeqDataSet()] object
 #' @param biomart_dataset A biomaRt dataset to use. To see the list, type
-#' \code{mart = useMart('ensembl')}, followed by \code{listDatasets(mart)}.
+#' `mart = useMart('ensembl')`, followed by `listDatasets(mart)`.
 #' @param idtype Character, the ID type of the genes as in the row names of
-#' \code{dds}, to be used for the call to \code{\link{getBM}}
+#' `dds`, to be used for the call to [getBM()]
 #'
-#' @return A data frame for ready use in \code{pcaExplorer}, retrieved from biomaRt.
+#' @return A data frame for ready use in `pcaExplorer`, retrieved from biomaRt.
 #' @export
 #'
 #' @examples
@@ -44,18 +44,18 @@ To obtain a list, type mart = useMart('ensembl'), followed by listDatasets(mart)
 
 #' Get an annotation data frame from org db packages
 #'
-#' @param dds A \code{\link{DESeqDataSet}} object
-#' @param orgdb_species Character string, named as the \code{org.XX.eg.db}
+#' @param dds A [DESeqDataSet()] object
+#' @param orgdb_species Character string, named as the `org.XX.eg.db`
 #' package which should be available in Bioconductor
 #' @param idtype Character, the ID type of the genes as in the row names of
-#' \code{dds}, to be used for the call to \code{\link{mapIds}}
+#' `dds`, to be used for the call to [mapIds()]
 #' @param key_for_genenames Character, corresponding to the column name for the 
 #' key in the orgDb package containing the official gene name (often called 
 #' gene symbol). 
 #' This parameter defaults to "SYMBOL", but can be adjusted in case the key is not
-#' found in the annotation package (e.g. for \code{org.Sc.sgd.db}).
+#' found in the annotation package (e.g. for `org.Sc.sgd.db`).
 #'
-#' @return A data frame for ready use in \code{pcaExplorer}, retrieved from the
+#' @return A data frame for ready use in `pcaExplorer`, retrieved from the
 #' org db packages
 #' @export
 #'

R/hi_loadings.R

@@ -1,16 +1,16 @@
 #' Extract genes with highest loadings
 #'
-#' @param pcaobj A \code{prcomp} object
+#' @param pcaobj A `prcomp` object
 #' @param whichpc An integer number, corresponding to the principal component of
 #' interest
 #' @param topN Integer, number of genes with top and bottom loadings
-#' @param exprTable A \code{matrix} object, e.g. the counts of a \code{\link{DESeqDataSet}}.
+#' @param exprTable A `matrix` object, e.g. the counts of a [DESeqDataSet()].
 #' If not NULL, returns the counts matrix for the selected genes
-#' @param annotation A \code{data.frame} object, with row.names as gene identifiers (e.g. ENSEMBL ids)
-#' and a column, \code{gene_name}, containing e.g. HGNC-based gene symbols
+#' @param annotation A `data.frame` object, with row.names as gene identifiers (e.g. ENSEMBL ids)
+#' and a column, `gene_name`, containing e.g. HGNC-based gene symbols
 #' @param title The title of the plot
 #'
-#' @return A ggplot2 object, or a \code{matrix}, if \code{exprTable} is not null
+#' @return A ggplot2 object, or a `matrix`, if `exprTable` is not null
 #'
 #' @examples
 #' dds <- makeExampleDESeqDataSet_multifac(betaSD = 3, betaSD_tissue = 1)

R/makeds.R

@@ -1,11 +1,11 @@
 #' Make a simulated DESeqDataSet for two or more experimental factors
 #'
 #' Constructs a simulated dataset of Negative Binomial data from different conditions.
-#' The fold changes between the conditions can be adjusted with the \code{betaSD_condition}
-#' and the \code{betaSD_tissue} arguments.
+#' The fold changes between the conditions can be adjusted with the `betaSD_condition`
+#' and the `betaSD_tissue` arguments.
 #'
 #' This function is designed and inspired following the proposal of
-#' \code{\link{makeExampleDESeqDataSet}} from the \code{DESeq2} package. Credits are given
+#' [makeExampleDESeqDataSet()] from the `DESeq2` package. Credits are given
 #' to Mike Love for the nice initial implementation
 #'
 #' @param n number of rows (genes)
@@ -15,10 +15,10 @@
 #' @param interceptMean the mean of the intercept betas (log2 scale)
 #' @param interceptSD the standard deviation of the intercept betas (log2 scale)
 #' @param dispMeanRel a function specifying the relationship of the dispersions on
-#' \code{2^trueIntercept}
+#' `2^trueIntercept`
 #' @param sizeFactors multiplicative factors for each sample
 #'
-#' @return a \code{\link{DESeqDataSet}} with true dispersion,
+#' @return a [DESeqDataSet()] with true dispersion,
 #' intercept for two factors (condition and tissue) and beta values in the
 #'  metadata columns.  Note that the true betas are provided on the log2 scale.
 #'

R/pair_corr.R

@@ -3,8 +3,8 @@
 #' @param df A data frame, containing the (raw/normalized/transformed) counts
 #' @param log Logical, whether to convert the input values to log2 (with addition
 #' of a pseudocount). Defaults to FALSE.
-#' @param method Character string, one of \code{pearson} (default), \code{kendall}, or
-#' \code{spearman} as in \code{cor}
+#' @param method Character string, one of `pearson` (default), `kendall`, or
+#' `spearman` as in `cor`
 #' @param use_subset Logical value. If TRUE, only 1000 values per sample will be used
 #' to speed up the plotting operations.
 #'