Description Usage Format Details Source References Examples
A dataset that contains genotypes simulated by gene drop based on a model of linkage disequilibrium fit to data from a candidate-gene case-control study. Several close relative pairs have been included in the simulated data.
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A list comprised of the following four objects:
[[1]] | snp.data | a snp.matrix object containing genotypes of 208 subjects (108 controls and 100 cases). |
Rows correspond to subjects and columns correspond to SNPs | ||
[[2]] | chromosome | a numeric vector containing the chromosome numbers of the SNPs |
[[3]] | physmap | a numeric vector of physical positions |
[[4]] | csct | a vector of case-control status (1=case, 0=control) |
The dataset contains mostly unrelated individuals, but includes two parent-offspring pairs and three full-siblings pairs to show how the CrypticIBDcheck package can be used to uncover cryptic relatedness.
The genotypes were simulated based on data from a candidate-gene case-control study described in Schuetz et al. (2012).
Schuetz JM, Daley D, Graham J, Berry BR, Gallagher RP, Connors JM, Gascoyne RD, Spinelli JJ, Brooks-Wilson AR (2012). Genetic Variation in Cell Death Genes and Risk of Non-Hodgkin Lymphoma. PLoS ONE, 7(2), e31560. doi:10.1371/journal.pone.0031560.
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Loading required package: rJPSGCS
Loading required package: rJava
Loading required package: chopsticks
Loading required package: survival
OpenJDK 64-Bit Server VM warning: Can't detect initial thread stack location - find_vma failed
Loading required package: car
Loading required package: ellipse
Attaching package: 'ellipse'
The following object is masked from 'package:car':
ellipse
Warning message:
In methods:::bind_activation(TRUE) :
methods:::bind_activation(TRUE) is deprecated;
you should rather provide methods for cbind2() / rbind2()
Warning message:
system call failed: Cannot allocate memory
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