check_duplicates: Checks for duplicated samples in snpRdata.

In hemstrow/snpR: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data

Checks for duplicated samples in snpRdata.

Description

Searches through a snpR dataset and, for every designated sample, determines the proportion of identical genotypes in every other sample. This function is not overwrite safe.

Usage

check_duplicates(x, y = 1:ncol(x), id.col = NULL, verbose = FALSE)

Arguments

x	snpRdata object
y	numeric or character, default 1:ncol(x). Designates the sample indices or IDs in x for which duplicates will be checked.
id.col	character, default NULL. Designates a column in the sample metadata which contains sample IDs. If provided, y is assumed to contain sample IDs uniquely matching those in the the sample ID column.
verbose	logical, default FALSE. If TRUE, prints detailed progress report.

Details

If an id column is specified, y should contain sample IDs matching those contained in that column. If not, y should contain sample indices instead. The proportion of identical genotypes between matching samples and all other samples are calculated. By default, every sample will be checked.

Value

A list containing:

• best_matches: Data.frame listing the best match for each sample noted in y and the percentage of genotypes identical between the two samples.

• data: A list containing the match proportion between each sample y and every sample in x, named for the samples y.

Author(s)

William Hemstrom

Examples

## Not run: 
# check for duplicates with sample 1
check_duplicates(stickSNPs, 1)

# check duplicates using the .samp.id column as sample IDs
check_duplicates(stickSNPs, 1, id.col = ".sample.id")

## End(Not run)

hemstrow/snpR documentation built on March 20, 2024, 7:03 a.m.