matchToCiteseq: Standardise names using the citeseq data set

In HelenLindsay/AbNames: Standardize Antibody Names

Standardise names using the citeseq data set

Description

Groups antibody names and selects the most frequent name. By default, the citeseq dataset is grouped by Antigen, Clone, Cat_Number (catalog number) and ALT_ID.

Usage

matchToCiteseq(x, cols = NULL, verbose = TRUE, check.matches = FALSE, ...)

Arguments

x	A data.frame or tibble containing a column "Antigen" to match to the citeseq data set
cols	(character(n), default NULL) Optional additional columns to use for matching in citeseq data set. ID columns from the citeseq dataset are used by default. Antibodies are grouped by a match in any of the ID columns.
verbose	Report which columns are used for matching? (default: TRUE)
check.matches	Set to TRUE to check which entries were matched (default FALSE)
...	Options passed on to getCommonName

Value

If check.matches is FALSE, the data.frame x is returned with an additional two columns "Antigen_std", containing the standardised name, and "n_matched", the number of entries used for deriving the standard name. The minimum value of "n_matched" is 1 and means that no matches were found.

If check.matches is TRUE, a grouped tibble is returned, containing rows from x grouped with rows from the citeseq data set that were matched. This can be used for checking whether matches are correct and identifying what was matched incorrectly if they are incorrect.

Author(s)

Helen Lindsay

Examples

df <- data.frame(Antigen = c("PD-L1", "CD3"))
matchToCiteseq(df)

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