Title: Finding Allele-Specific Copy Number in Next-Generation

Title: Finding Allele-Specific Copy Number in Whole-Exome Sequencing
Description: This is a method for Allele-specific DNA Copy Number profiling for whole-Exome sequencing data.  Given the allele-specific coverage and site biases at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number.  It requires, as input, the read counts for each variant allele in a pair of case and control samples, as well as the site biases. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.

Description: This is a method for Allele-specific DNA Copy Number profiling for whole-Exome sequencing data.  Given the allele-specific coverage and site biases at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number.  It requires, as input, the read counts for each variant allele in a pair of case and control samples, as well as the site biases. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.  The implemented method is based on the paper: Chen, H., Jiang, Y., Maxwell, K., Nathanson, K. and Zhang, N. (under review). Allele-specific copy number estimation by whole Exome sequencing.

Description: A value is falsy if it is NULL, FALSE, the empty string,
zero, or an empty vector or list. Other values are truthy. The new
%&&% and %||% operators work with falsy and truthy values and
can be used for concise conditional execution.
Packaged: 2015-04-08 15:30:21 UTC; gaborcsardi

Packaged: 2014-08-27 16:10:35 UTC; gaborcsardi

Description: Given vectors of family sizes and number of affecteds per family, calculates the risk of disease recurrence in an unaffected person, conditional on a family having at least k affected members. Methods also model heterogeneity of disease risk across families by fitting a mixture model, allowing for high and low risk families.