report_pipe: Report an object of pipeline classes.
In markgene/yamatCN: Yet Another Methylation Array Toolkit Copy Number Analysis

Description Usage Arguments Value Methods (by class)

Report an object of pipeline classes.

report_pipe(x, outdir, genome_plot_file = "genome-plot.png",
  genome_plot_width = 9, genome_plot_height = 15, chr_per_row = 4,
  chr_plot_width = 9, chr_plot_height = 6, size = 5e+06,
  cn_boundary = c(1.319508, 2.828427), segment_file = "segments.tab",
  igv_segment_file = "igv-segments.tab",
  shiny_segment_file = "shiny-segments.tab", overwrite = FALSE,
  verbose = TRUE, ...)

## S4 method for signature 'CwobPipe'
report_pipe(x, outdir,
  genome_plot_file = "genome-plot-cwob.png", genome_plot_width = 9,
  genome_plot_height = 15, chr_per_row = 4, chr_plot_width = 9,
  chr_plot_height = 6, size = 5e+06, cn_boundary = c(1.319508,
  2.828427), segment_file = "segments-cwob.tab",
  igv_segment_file = "igv-segments-cwob.tab", overwrite = FALSE,
  verbose = TRUE)

## S4 method for signature 'ConumeePipe'
report_pipe(x, outdir,
  genome_plot_file = "genome-plot.png", genome_plot_width = 9,
  genome_plot_height = 15, chr_per_row = 4, chr_plot_width = 9,
  chr_plot_height = 6, size = 5e+06, CNscale = "absolute",
  cn_boundary = c(1.319508, 2.828427), segment_file = "segments.tab",
  igv_segment_file = "igv-segments.tab",
  shiny_segment_file = "shiny-segments.tab", detail_plot_height = 7,
  detail_plot_width = 5, max_cn = 6, overwrite = FALSE,
  verbose = TRUE)

`x`	An object.
`outdir`	A character scalar of output directory.
`genome_plot_file`	A character scalar of the genome plot file which shows all chromosomes.
`genome_plot_width`	An integer scalar. Default to 9.
`genome_plot_height`	An integer scalar. Default to 15.
`chr_per_row`	An integer scalar of the number of chromosomes per row in genome plot. Default to 4.
`chr_plot_width`	An integer scalar of the width of individual chromosome plot. Default to 9.
`chr_plot_height`	An integer scalar of the height of individual chromosome plot. Default to 6.
`size`	An integer scalar of the threshold to define CNVs. Default to `5e6` (5 Mb).
`cn_boundary`	An numeric vector of length two which defines the boundaries to define CNVs. If a segment has a segment mean lower than the first element or higher than the second element, it is a CNV. It is the absolute value, so 2 means no copy number change. Default to `c(1.319508, 2.828427)`.
`segment_file`	A character scalar of segments file which is a table of segments. Default to "segments-cwob.tab".
`igv_segment_file`	A character scalar of segments file which is a table of segments. Default to "igv-segments.tab".
`shiny_segment_file`	A character scalar of segments file which is a table of segments. Default to "shiny-segments.tab".
`overwrite`	A logical scalar. Default to FALSE.
`verbose`	A logical scalar. Default to TRUE.
`...`	Any other arguments.
`CNscale`	Character string specifying if copy number calls supplied are relative (i.e.copy neutral == 0) or absolute (i.e. copy neutral ==2). One of "relative" or "absolute".
`detail_plot_height`	An integer scalar. Default to 7.
`detail_plot_width`	An integer scalar. Default to 5.
`max_cn`	A numeric scalar of the maximum of CN. The CNs are sometime extremely large. The will remove the data points whose CN are greater than `max_cn`. Default to 6.