readGPR: Read GPR File
In pkimes/upbm: Tools for the analysis of universal protein binding microarrays

Description Usage Arguments Details Value Author(s)

Helper function for reading in a single GPR file.

readGPR(
  gpr_path,
  gpr_type,
  useMedian = TRUE,
  filterFlags = TRUE,
  readBackground = TRUE
)

`gpr_path`	path to GPR file.
`gpr_type`	scan type; one of "Alexa", "Cy3", "Masliner".
`useMedian`	logical whether to use median fluorescent intensity for each probe rather than mean fluorescent intensity. (default = TRUE)
`filterFlags`	logical whether to replace intensity values at probes flagged manually or automatically as being low quality. ('Bad': -100, 'Absent': -75, 'Not Found': -50) with NA. (default = TRUE)
`readBackground`	logical whether to also read in probe background intensities. (default = TRUE)

Since the names of foreground and background columns can vary across samples, they are identified using regular expressions. Therefore, if the column names deviate from the expected format ("F.* Mean", "F.* Median". "B.* Mean", "B.* Median"), the function may fail to read the foreground and background intensities.

tibble (data.frame-like) object of a single GPR file with three or four columns: 'Column', 'Row', 'foreground', (optionally) 'background'. ('ID' and 'Name' columns are ignored as these may be incorrect in the GPR file.)

Patrick Kimes

pkimes/upbm documentation built on Oct. 17, 2020, 9:10 a.m.