save_sestats: Save SE contrast stats output
In jmw86069/jamses: Jam SummarizedExperiment Stats

save_sestats

R Documentation

Save SE contrast stats output

Description

Save SE contrast stats output

Usage

save_sestats(
  sestats,
  file = NULL,
  assay_names = NULL,
  contrast_names = NULL,
  cutoff_names = NULL,
  type = c("xlsx", "list"),
  data_content = c("data", "hits"),
  max_nchar_sheetname = 31,
  review_output = TRUE,
  sheet_prefix = NULL,
  use_assay_suffix = TRUE,
  width_factor = 1,
  max_rows = NULL,
  colorSub = NULL,
  rename_contrasts = TRUE,
  se = NULL,
  rowData_colnames = NULL,
  row_type = "gene_name",
  hitRule = c(-1, 0, 1),
  hitFormat = "#,##0",
  freezePaneColumn = 2,
  verbose = FALSE,
  ...
)

Arguments

`sestats`	`list` object output from `se_contrast_stats()`
`file`	`character` string indicating the filename to save. When `file` is `NULL`, output is returned as a `list`, equivalent to `type="list"`.
`assay_names`	`character` string indicating which assay names to save, stored in `dimnames(sestats$hit_array)$Signal`. When `NULL` then all assay names are saved.
`contrast_names`	`character` string indicating which contrasts to save, stored in `dimnames(sestats$hit_array)$Contrasts`. The default `NULL` will save all contrasts.
`type`	`character` string indicating the type of file to save. `"xlsx"` - saves an Excel xlsx file using `jamba::writeOpenxlsx()`. Each worksheet is renamed so the string length does not exceed `max_nchar_sheetname`, whose default is 31 characters. `"list"` - returns a `list` of `data.frame` objects, equivalent to the data to be stored in an output file. This option will not save data to `file`.
`data_content`	`character` string describing the data content to include: `⁠"contrasts","hits"⁠` - include worksheets per `contrast_names`, then assemble one `"hit sheet"` across all contrasts. One hit sheet is created for each value in `assay_names`. `"contrasts"` - (default) include worksheets per `contrast_names` `"hits"` - include only one `"hit sheet"` per value in `assay_names`.
`max_nchar_sheetname`	`integer` number of characters allowed in Microsoft Excel worksheet names, default 31 characters.
`review_output`	`logical` indicating whether a summary of output should be returned as a `data.frame` without exporting data. This summary will indicate all worksheets to be saved, in addition to the sheetName for each worksheet.
`sheet_prefix`	`character` string with optional character prefix to use when creating worksheet names.
`use_assay_suffix`	`logical` indicating whether to include `assay_names` as suffix when forming sheet names, when there is more than one unique assay name to be saved. This step will attempt to abbreviate `assay_names` by taking up to 4 characters from each word in the assay name, where each word is delimited by `"[-.:_ ]+"`. Otherwise, sheet names are forced to be unique by taking a substring of the contrast name of up to `max_nchar_sheetname`, passing any duplicate strings to `jamba::makeNames()` with suffix `"_v"` followed by an integer number.
`width_factor`	`numeric` used to adjust relative column widths in the output Excel worksheets.
`colorSub`	`character` vector of colors, optional, used to define categorical background colors for text string fields in Excel. The `names(colorSub)` are matched to character strings to assign colors.
`hitRule`, `hitFormat`, `freezePaneColumn`	arguments passed to `jamba::writeOpenxlsx()`.
`verbose`	`logical` indicating whether to print verbose output.
`...`	additional arguments are passed to `jamba::writeOpenxlsx()`