getCommonName: Find most common antibody name

In HelenLindsay/AbNames: Standardize Antibody Names

Find most common antibody name

Description

Find most common name by matching any/all of Antigen name, clone, gene identifiers

Usage

getCommonName(
  x,
  cols = NULL,
  ab = "Antigen",
  fill_col = "Antigen_std",
  n_matched = "n_matched",
  ignore = TRUE,
  verbose = TRUE,
  ...
)

Arguments

x	data.frame for finding common name
cols	Columns for grouping, default: NULL means that the columns Antigen, Cat_Number, Clone, ALT_ID are used. Note that gene identifiers are not used by default as some antibodies target particular isoforms.
ab	Column containing antibody names for standardising, default "Antigen"
fill_col	column to add
n_matched	name of column to add with number of matching results, default "n_matched"
ignore	A named list, where names match colnames of x and values are regular expressions matching values in x that should not be used for grouping. For example, entries where the catalogue number is "Custom made" should not be used for matching. Alternatively, set to TRUE to use the default ignore patterns.
verbose	Print information about which columns are used for grouping? Default: TRUE
...	pass keep = TRUE for keeping grouping columns for debugging

Details

Be careful of exceptions, e.g. Cat_Number == "custom made"

Author(s)

Helen Lindsay

HelenLindsay/AbNames documentation built on June 6, 2023, 1:18 p.m.