extract_metadata: Pull metadata from a table (xlsx/xls/csv/whatever)

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Pull metadata from a table (xlsx/xls/csv/whatever)

Description

I find that when I acquire metadata from a paper or collaborator, annoyingly often there are many special characters or other shenanigans in the column names. This function performs some simple sanitizations. In addition, if I give it a filename it calls my generic 'read_metadata()' function before sanitizing.

Usage

extract_metadata(
  metadata,
  id_column = "sampleid",
  fill = NULL,
  fill_condition = TRUE,
  fill_batch = TRUE,
  sanitize = TRUE,
  ...
)

Arguments

metadata	file or df of metadata
id_column	Column in the metadat containing the sample names.
fill	Fill missing data with this.
fill_condition	Add a condition column if there is not one?
fill_batch	Add a batch column if there is not one?
sanitize	Perform my various sanitizers on the data?
...	Arguments to pass to the child functions (read_csv etc).

Value

Metadata dataframe hopefully cleaned up to not be obnoxious.

Examples

 ## Not run: 
  sanitized <- extract_metadata("some_random_supplemental.xls")
  saniclean <- extract_metadata(some_goofy_df)

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.