Add more examples

R/runPDTMTAnalysis.R

@@ -205,20 +205,30 @@
 #'
 #' @examples
 #' if (interactive()) {
-#' #    sampleAnnot <- read.delim(
-#' #        system.file("extdata/mq_example/1356_sampleAnnot.txt",
-#' #                                          package = "einprot"))
-#' #    ## Basic analysis
-#' #    out <- runPDTMTAnalysis(
-#' #        outputDir = tempdir(),
-#' #        outputBaseName = "PD_TMT_basic",
-#' #        species = "mouse",
-#' #        iColPattern = "",
-#' #        sampleAnnot = sampleAnnot,
-#' #        stringIdCol = NULL
-#' #    )
-#' #    ## Output file
-#' #    out
+#'     ## Basic analysis
+#'     out <- runPDTMTAnalysis(
+#'         outputDir = tempdir(),
+#'         outputBaseName = "PD_TMT_basic",
+#'         species = "baker's yeast",
+#'         iColPattern = "^Abundance.F.+.Sample.",
+#'         pdOutputFolder = system.file("extdata", "pdtmt_example",
+#'                                      package = "einprot"),
+#'         pdResultName = "Fig2_m23139_RTS_QC_varMods",
+#'         inputLevel = "Proteins",
+#'         pdAnalysisFile = system.file("extdata", "pdtmt_example",
+#'                           "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
+#'                           package = "einprot"),
+#'         sampleAnnot = data.frame(
+#'             sample = c("HIS4KO_S05", "HIS4KO_S06", "HIS4KO_S07", "HIS4KO_S08",
+#'                        "MET6KO_S01", "MET6KO_S02", "MET6KO_S03", "MET6KO_S04",
+#'                        "URA2KO_S09", "URA2KO_S10", "URA2KO_S11", "URA2KO_S12",
+#'                        "WT_S13", "WT_S14", "WT_S15", "WT_S16"),
+#'             group = c(rep("HIS4KO", 4), rep("MET6KO", 4), rep("URA2KO", 4),
+#'                       rep("WT", 4))),
+#'         stringIdCol = NULL
+#'     )
+#'     ## Output file
+#'     out
 #' }
 #'
 #' @returns Invisibly, the path to the compiled html report.

R/seqLogoApp.R

@@ -17,6 +17,14 @@
 #'     files exported from the shiny app.
 #' @param ... Additional arguments passed to \code{utils::read.csv}.
 #'
+#' @examples
+#' tbl <- data.frame(id = c("seq1", "seq2", "seq3"),
+#'                   seqWindow = c("LITKDHE", "RQMKQPE", "LSNKVHG"))
+#' tfile <- tempfile(fileext = "_seq.csv")
+#' write.table(tbl, file = tfile, row.names = FALSE,
+#'             col.names = TRUE, quote = TRUE, sep = ",")
+#' seqLogoApp(tfile)
+#'
 #' @importFrom shiny fluidPage fluidPage sidebarLayout sidebarPanel
 #'     mainPanel downloadButton plotOutput renderPlot reactive downloadHandler
 #'     shinyApp textOutput renderText

R/subtractBaseline.R

@@ -20,6 +20,20 @@
 #'
 #' @returns Matrix with baseline-subtracted abundances.
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#'
+#' ## Introduce artificial batch column
+#' sce$batch <- rep(c("B1", "B2", "B3"), 3)
+#' SummarizedExperiment::colData(sce)
+#' mat <- getMatSubtractedBaseline(sce, assayName = "log2_LFQ.intensity",
+#'                                 baselineGroup = "RBC_ctrl",
+#'                                 sceFull = sce)
+#' ## After the subtraction, the baseline samples are equalized across the
+#' ## different batches
+#' head(mat)
+#'
 #' @importFrom SummarizedExperiment assay assayNames
 #'
 getMatSubtractedBaseline <- function(sce, assayName, baselineGroup, sceFull) {