gtoxReport: Generate a report

In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data

Generate a report

Description

gtoxReport generates a report.

Usage

gtoxReport(type, asid, params = NULL, odir = getwd(), report_author,
  report_title = "Report", sumfile = NULL,
  keep.intermediates = FALSE)

Arguments

type	The type of report to generate
asid	The assay source/study ID
params	Named list containing report type-specific parameters, see details
odir	The output directory
report_author	The author for the report
report_title	The title for the report
sumfile	Path to a text file that inserts into the report
keep.intermediates	TRUE/FALSE, keep intermediate files when TRUE

Details

'type' can have three values, "all," "compare," or "qc." Each report contains slightly different elements, but in general:

• "all" – summarizes the results for all or some compounds

  • "chids" – (optional) a vector of chid values to report, rather than all available compounds

• "compare" – compares the results for two compounds

  • "c1" – (required) the chid for the first compound to compare

  • "c2" – (required) the chid for the second compound to compare

• "qc" – summarizes low-level data for quality control purposes

  • "aids" – (optional) a vector of aid values to report, rather than all available assays

The required list elements vary depending on the type of report, and are described under the report descriptions above.

'sumfile' allows the user to inject a Tex file into the report. The file contents will be inserted into the Study Overview section, immediately after the autogenerated text. Technically, 'sumfile' is brewed, so 'sumfile' can make use of brew and Sweave syntax, and all data loaded for the report.

Value

None

Examples

## Generate full analysis report

## Not run: 
## Generate report
gtoxReport(type = "all", asid = 1L, report_author = "author", 
report_title = "Processing report")

## End(Not run)

pmpsa-hpc/GladiaTOX documentation built on Sept. 1, 2023, 5:52 p.m.