qtl2 (version 0.32)

get_common_ids: Get common set of IDs from objects

Description

For a set objects with IDs as row names (or, for a vector, just names), find the IDs that are present in all of the objects.

Usage

get_common_ids(..., complete.cases = FALSE)

Value

A vector of character strings for the individuals that are in common.

Arguments

...

A set of objects: vectors, lists, matrices, data frames, and/or arrays. If one is a character vector with no names attribute, it's taken to be a set of IDs, itself.

complete.cases

If TRUE, look at matrices and non-character vectors and keep only individuals with no missing values.

Details

This is used (mostly internally) to align phenotypes, genotype probabilities, and covariates in preparation for a genome scan. The complete.cases argument is used to omit individuals with any missing covariate values.

Examples

x <- matrix(0, nrow=10, ncol=5); rownames(x) <- LETTERS[1:10]
y <- matrix(0, nrow=5, ncol=5);  rownames(y) <- LETTERS[(1:5)+7]
z <- LETTERS[5:15]
get_common_ids(x, y, z)

x[8,1] <- NA
get_common_ids(x, y, z)
get_common_ids(x, y, z, complete.cases=TRUE)