trio.data: Case-Parent Trio Data

In trio: Testing of SNPs and SNP Interactions in Case-Parent Trio Studies

Description

trio.data contains several simulated data sets used in the different examples for the analyses with the functions in the R package trio.

For the applications of genotypic TDTs for individual SNPs and two-way interactions with, for example, tdt and tdt2way, respectively, trio.data contains a 300 x 6 matrix called mat.test consisting of genotype data for 100 trios genotyped at 6 SNPs.

For the application of probTDT to genotype probabilities, trio.data contains a 334 x 180 matrix called prob.mat.test containing genotype probabilities for 334 SNPs and 20 trios.

For the preparation of the trio data for an application of trio logic regression with trio.check and trio.prepare, trio.data contains different data set containing genotype data for 10 SNPs in 100 trios in different formats.

trio.gen1, trio.gen2, and trio.gen.err consist of 12 columns and 300 rows, where the first two columns contain family identifier and individual identifier. In the columns afterwards, each SNPs is encoded in one variable denoting the number of minor alleles.

trio.ped1, trio.ped2, and trio.ped.err consist of 26 columns and 300 rows, where the first six columns identify the family structure of the data, and the phenotype. Besides the variables providing information on the family structure and the phenotypes (columns 1 to 6), each SNPs is encoded in two variables denoting the alleles.

Contrary to the other data sets, trio.gen.err and trio.ped.err contain Mendelian errors.

For the application of the functions getLD and findLDblocks for computing the pairwise LD values and for detecting the LD blocks, respectively, trio.data contains a 500 x 50 matrix called LDblock that is composed of genotype data for 10 LD blocks each consisting of 5 SNPs in strong LD.

Finally, for the simulation of trio data with trio.sim, trio.data contains examples for haplotype frequencies used in these simulations. Both freq.hap and simuBkMap are data.frames containing haplotype information, including the haplotype block identifier, haplotype, and haplotype frequency. While freq.hap is a data frame consisting of 20 rows and 3 columns, simuBkMap consists of 66 rows and 3 columns. step3way is a list internally used for simulation, containing some indexes and sampling frequencies.

Author(s)

LDdata and mat.test: Holger Schwender, [e-mail]; prob.mat.test: Margaret Taub, [e-mail]; all other data sets: Qing Li, [e-mail]

Examples

# Data can be loaded by
data(trio.data)

Example output

trio documentation built on Nov. 8, 2020, 7:41 p.m.