raw.data: Synthetic dataset containing single nucleotide polymorphisms...

In kridsadakorn/ipcaps.bioc: Iterative Pruning to Capture Population Structure

Description

The raw.data is the simulated dataset which consists of 3,000 independent SNPs and 1,004 individuals belonging to one of 5 populations (200 individuals each) and 4 outlying individuals. The matrix raw.data contains the number 0, 1, and 2 representing SNP in additive coding. The pairwise genetic distance between populations are listed below (see Balding, 1995):

	pop1	pop2	pop3	pop4	pop5
pop1		0.0040	0.0059	0.0085	0.0101
pop2	0.0040		0.0055	0.0082	0.0099
pop3	0.0059	0.0055		0.0104	0.0119
pop4	0.0085	0.0082	0.0104		0.0139
pop5	0.0101	0.0099	0.0119	0.0139

Usage

data(ipcaps_example)

Format

A matrix with 3,000 columns and 1,004 rows

References

Balding, D.J., and Nichols, R.A. (1995). A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96, 3-12.

See Also

label and PC

kridsadakorn/ipcaps.bioc documentation built on Jan. 22, 2020, 11:18 p.m.