Generate countsimQC report — countsimQCReport • countsimQC

Generate a report comparing a range of characteristics across a collection of one or more count data sets.

countsimQCReport(
  ddsList,
  outputFile,
  outputDir = "./",
  outputFormat = NULL,
  showCode = FALSE,
  rmdTemplate = NULL,
  forceOverwrite = FALSE,
  savePlots = FALSE,
  description = NULL,
  maxNForCorr = 500,
  maxNForDisp = Inf,
  calculateStatistics = TRUE,
  subsampleSize = 500,
  kfrac = 0.01,
  kmin = 5,
  permutationPvalues = FALSE,
  nPermutations = NULL,
  knitrProgress = FALSE,
  quiet = FALSE,
  ignorePandoc = FALSE,
  useRAGG = FALSE,
  dpi = 96,
  ...
)

Arguments

ddsList: Named list of DESeqDataSets or count matrices to compare. See the DESeq2 Bioconductor package (http://bioconductor.org/packages/release/bioc/html/DESeq2.html) for more information about the DESeqDataSet class. Each DESeqDataSet object in the list should contain a count matrix, a data frame with sample information and a design formula. The sample information and design formula will be used to calculate dispersions appropriately. If count matrices are provided, it is assumed that all columns represent replicate samples, and the design formula ~1 will be used.
outputFile: The file name of the final report. The extension must match the selected outputFormat (i.e., either .html or .pdf).
outputDir: The directory where the final report should be saved.
outputFormat: The output format of the report. If set to NULL or "html_document", an html report will be generated. If set to "pdf_document", a pdf report will be generated.
showCode: Whether or not to include the code in the final report.
rmdTemplate: The Rmarkdown (.Rmd) file that will be used as the template for generating the report. If set to NULL (default), the template provided with the countsimQC package will be used. See Details for more information.
forceOverwrite: Whether to force overwrite existing output files when saving the generated report and figures.
savePlots: Whether to save the ggplot objects for all the output figures, to allow additional fine-tuning and generation of individual plots. Note that the resulting file can be quite large, especially when many and/or large data sets are compared.
description: A string (of arbitrary length) describing the content of the generated report. This will be included in the beginning of the report. If set to NULL, a default description listing the number and names of the included data sets will be used.
maxNForCorr: The maximal number of samples (features) for which pairwise correlation coefficients will be calculated. If the number of samples (features) exceeds this number, they will be randomly subsampled.
maxNForDisp: The maximal number of samples that will be used to estimate dispersions. By default, all samples are used. This can be lowered to speed up calculations (and obtain approximate results) for large data sets.
calculateStatistics: Whether to calculate quantitative pairwise statistics for comparing data sets in addition to generating the plots.
subsampleSize: The number of randomly selected observations (samples, features or pairs of samples or features) for which certain (time-consuming) statistics will be calculated. Only used if calculateStatistics = TRUE.
kmin, kfrac: For statistics that require the extraction of the k nearest neighbors of a given point, the number of neighbors will be max(kmin, kfrac * nrow(df))
permutationPvalues: Whether to calculate permutation p-values for selected pairwise data set comparison statistics.
nPermutations: The number of permutations to perform when calculating permutation p-values for data set comparison statistics. Only used if permutationPvalues = TRUE.
knitrProgress: Whether to show the progress bar when the report is generated.
quiet: Whether to suppress warnings and progress messages when the report is generated.
ignorePandoc: Determines what to do if pandoc or pandoc-citeproc is missing (if Sys.which("pandoc") or Sys.which("pandoc-citeproc") is ""). If ignorePandoc is TRUE, only a warning is given. The figures will be generated, but not the final report. If ignorePandoc is FALSE (default), the execution stops immediately.
useRAGG: Logical scalar, indicating whether to use ragg_png as the graphics device in the report rather than the default png.
dpi: Numeric scalar, setting the dpi of the generated plots. Only used if useRAGG is TRUE.
...: Other arguments that will be passed to rmarkdown::render.

Value

No value is returned, but a report is generated in the outputDir directory.

Details

When the function is called, the template file (specified by rmdTemplate) will be copied into the output folder, and rmarkdown::render will be called to generate the final report. If there is already a .Rmd file with the same name in the output folder, the function will raise an error and stop, to avoid overwriting the existing file. The reason for this behaviour is that the copied template in the output folder will be deleted once the report is generated.

Author

Charlotte Soneson

Examples

## Load example data
data(countsimExample)
if (FALSE) { # \dontrun{
## Generate report
countsimQCReport(countsimExample, outputDir = "./",
                 outputFile = "example.html")
} # }