Package ‘ trio ’
نویسندگان
چکیده
Description Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.
منابع مشابه
Package 'trio' Title Testing of Snps and Snp Interactions in Case-parent Trio Studies
Description Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent tr...
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Description The package contains functions that 1) estimates gene-environment interaction between a SNP and a continuous non-genetic attribute by fitting a generalized additive model to case-parent trio data, 2) produces graphical displays of estimated interaction, 3) performs permutation test of gene-environment interaction; 4) simulates informative case-parent trios.
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The starting point for this section of the vignette are B allele frequencies and log R ratios that are available from software such as GenomeStudio and the R package crlmm. In this section, we assume that the low-level summaries are available in a plain text file – one file per sample. For users of the crlmm package for preprocessing, please refer to the crlmmDownstream vignette. To illustrate ...
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For the analysis of case-parent trio genotyping arrays, copy number variants (CNV) appearing in the offspring that differ from the parental copy numbers are often of interest (de novo CNV). This package defines a statistic, referred to as the minimum distance, for identifying de novo copy number alterations in the offspring. We smooth the minimum distance using the circular binary segmentation ...
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