extract_snpRdata: Get from or overwrite components of a snpRdata object

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

Get from or overwrite components of a snpRdata object

Description

Fetch or overwrite the major parts of a snpRdata object (genotypes, snp meta, or sample meta). If overwritten, any calculated stats will be removed, since their values may be dependant upon changes in metadata.

Usage

## S4 method for signature 'snpRdata'
genotypes(x)

## S4 replacement method for signature 'snpRdata'
genotypes(x) <- value

## S4 method for signature 'snpRdata'
snp.meta(x, value)

## S4 replacement method for signature 'snpRdata'
snp.meta(x) <- value

## S4 method for signature 'snpRdata'
sample.meta(x, value)

## S4 replacement method for signature 'snpRdata'
sample.meta(x) <- value

Arguments

x	snpRdata object to get genotype data from.
value	Genotypes, snp metadata, or sample metadata

Functions

• genotypes(snpRdata): view genotypes

• genotypes(snpRdata) <- value: set genotypes

• snp.meta(snpRdata): view snp meta

• snp.meta(snpRdata) <- value: set snp meta

• sample.meta(snpRdata): view sample meta

• sample.meta(snpRdata) <- value: set sample meta

Examples

# copy test data
test <- stickSNPs

# show genotypes
genotypes(test)

# show or overwrite snp meta
snp.meta(test)
snp.meta(test) <- data.frame(pos = sample(10000, nrow(test), replace = TRUE),
                             chr = sample(LETTERS[1:4], nrow(test), 
                                          replace = TRUE))

#show or overwrite sample meta
sample.meta(test)
sample.meta(test) <- data.frame(fam = sample(LETTERS[1:4], ncol(test), 
                                             replace = TRUE), 
                                pop = sample(LETTERS[5:8], ncol(test), 
                                             replace = TRUE))

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