ambiguity: Inspect the ambiguity of a mapping

In saezlab/OmnipathR: OmniPath web service client and more

Inspect the ambiguity of a mapping

Description

Inspect the ambiguity of a mapping

Usage

ambiguity(
  d,
  from_col,
  to_col,
  groups = NULL,
  quantify = TRUE,
  qualify = TRUE,
  expand = NULL,
  global = FALSE,
  summary = FALSE
)

Arguments

d	Data frame: a data frame with two columns to be inspected. It might contain arbitrary other columns. Existing grouping will be removed.
groups	Character vector of column names. Inspect ambiguity within these groups; by default, ambiguity is determined across all rows.
quantify	Logical or character: inspect the mappings for each ID for ambiguity. If TRUE, for each translated column, two new columns will be created with numeric values, representing the ambiguity of the mapping on the "from" and "to" side of the translation, respectively. If a character value provided, it will be used as a column name suffix for the new columns.
qualify	Logical or character: inspect the mappings for each ID for ambiguity. If TRUE, for each translated column, a new column will be inculded with values 'one-to-one', 'one-to-many', 'many-to-one' or 'many-to-many'. If a character value provided, it will be used as a column name suffix for the new column.
expand	Logical: override the expansion of target columns, including 'to_col': by default, this function expands data into multiple rows if the 'to_col' has already been expanded. Using this argument, the 'to_col' and other target columns will be lists of vectors for 'expand = FALSE', and simple vectors for 'expand = TRUE'.
global	Logical or character: if 'groups' are provided, analyse ambiguity also globally, across the whole data frame. Character value provides a custom suffix for the columns quantifying and qualifying global ambiguity.
summary	Logical: generate a summary about the ambiguity of the translation and make it available as an attribute.

Value

A data frame (tibble) with ambiguity information added in new columns, as described at the "quantify" and "qualify" arguments.

saezlab/OmnipathR documentation built on Feb. 4, 2025, 5:42 p.m.