posted 2 projects.
hapFabia is an R package for identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data.
Initial Announcement on mloss.org.
FABIA is a biclustering algorithm that clusters rows and columns of a matrix simultaneously. Consequently, members of a row cluster are similar to each other on a subset of columns and, analogously, members of a column cluster are similar to each other on a subset of rows.
Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns.
Applications include detection of transcriptional modules in gene expression data and identification of haplotypes/>identity by descent< consisting of rare variants obtained by next generation sequencing.
CHANGES IN VERSION 2.4.0
o spfabia bugfixes
CHANGES IN VERSION 2.3.1
o Getters and setters for class Factorization
spfabia: fabia for a sparse data matrix (in sparse matrix
format) and sparse vector/matrix computations in the code
to speed up computations.
(a) detecting >identity by descent< in next generation
sequencing data with rare variants,
(b) detecting >shared haplotypes< in disease studies based
on next generation sequencing data with rare variants;
fabia for non-negative factorization (parameter: non_negative);
changed to C and removed dependencies to Rcpp;
improved update for lambda (alpha should be smaller, e.g. 0.03);
introduced maximal number of row elements (lL);
introduced cycle bL when upper bounds nL or lL are effective;
reduced computational complexity;
(a) update formula for lambda: tighter approximation,
(b) corrected inverse of the conditional covariance matrix of z;
New option nL: maximal number of biclusters per row element;
Sort biclusters according to information content;
Improved and extended preprocessing;
Update to R2.13