write_textfiles_to_share: Text files to share
In Rundmus/BAf-R_package: Binder Array data hanlding package in facility

Description Usage Arguments Functions Author(s) See Also

View source: R/write_textfiles_to_share.R

Write text files to share the data stored in a BAf-class object with collaborators

write_textfiles_to_share(
  baf,
  prefix = "BAf",
  suffix = paste0("(", Sys.Date(), ")"),
  path = "_sent",
  fn_data = "-data",
  fn_sample = NULL,
  fn_binder = NULL,
  incl_sample_i = c("id"),
  incl_binder_i = c("id"),
  fix_sid = c(),
  quote = TRUE,
  sep = "\t"
)

write_textfiles_to_share.SBA(
  baf,
  prefix = "SBA",
  suffix = paste0("(", Sys.Date(), ")"),
  path = "_sent",
  fn_data = "-data",
  fn_sample = NULL,
  fn_binder = NULL,
  incl_sample_i = c("id"),
  incl_binder_i = c("id", "gene_name", "gene_description", "ensg_id"),
  fix_sid = c(NEG_CTRL = "EMPTY-0001", REPEATED_SAMPLE = "MIX_1-0001"),
  quote = TRUE,
  sep = "\t"
)

`baf`	an object of the `BAf-class`, of which the data will be converted to text files
`prefix`	prefix used in file name. An ID for sample set is recommended.
`suffix`	the suffix in the file name
`path`	where those files should be saved.
`fn_data`	the characters added into the name of the BAf MFI data file to indicate it contains data (e.g '-data')
`fn_sample, fn_binder`	the characters added into the name of the file of sample/binder information. If this is NULL as the default, the file will be not generated.
`incl_sample_i, incl_binder_i`	the columns in BAf@sinfo/@binder that will be included in 'data'/'binder' file. The column for sample IDs at least should be included in `incl_sample_i`.
`fix_sid`	a named vector of characters. The sample IDs that match to any of those characters will be replaced with the corresponding name in this vector. An examples is `c(NEG_CTRL = "EMPTY-0001", REPEATED_SAMPLE = "MIX_1-0001")`
`quote`	same as `quote` in `write.table`. Default is TRUE
`sep`	seperator in the output text files. Tab is the default.