amplicanReport: Prepare reports as .Rmd files.
In amplican: Automated analysis of CRISPR experiments

Description Usage Arguments Value See Also Examples

amplicanReport takes a configuration file, fastq reads and output directory to prepare summaries as an editable .Rmd file. You can specify whether you want to make summaries based on ID, Barcode, Group or even guideRNA and Amplicon. This function automatically knits all reports after creation. If you want to postpone knitting and edit reports, use .Rmd templates to create your own version of reports instead of this function.

amplicanReport(results_folder, levels = c("id", "barcode", "group",
  "guide", "amplicon", "summary"), report_files = c("id_report",
  "barcode_report", "group_report", "guide_report", "amplicon_report",
  "index"), cut_buffer = 5, xlab_spacing = 4, top = 5,
  knit_reports = TRUE)

`results_folder`	(string) Folder containing results from the `amplicanAlign` function, do not change names of the files.
`levels`	(vector) Possible values are: "id", "barcode", "group", "guide", "amplicon", "summary". You can also input more than one value eg. c("id", "barcode") will create two separate reports for each level.
`report_files`	(vector) You can supply your own names of the files. For each of the levels there has to be one file name. Files are created in current working directory by default.
`cut_buffer`	(numeric) Default 5. A number of bases that is used around the specified cut site.
`xlab_spacing`	(numeric) Default is 4. Spacing of the ticks on the x axis of plots.
`top`	(numeric) Default is 5. How many of the top most frequent unassigned reads to report? It is only relevant when you used forward and reverse reads. We align them to each other as we could not specify correct amplicon.
`knit_reports`	(boolean) Whether to knit reports automatically.

(string) Path to the folder with results.

Other analysis steps: amplicanAlign, amplicanConsensus, amplicanFilter, amplicanMap, amplicanNormalize, amplicanOverlap, amplicanPipelineConservative, amplicanPipeline, amplicanSummarize

results_folder <- tempdir()
amplicanReport(results_folder, report_files = file.path(results_folder,
                                                        c("id_report",
                                                          "barcode_report",
                                                          "group_report",
                                                          "guide_report",
                                                          "amplicon_report",
                                                          "index")),
               knit_reports = FALSE)