Haplin

Package: Haplin
Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Version: 6.0.1
Date: 2016-05-25
Type: Package
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@fhi.no>
Depends: GenABEL, DatABEL
Imports: utils, stats, graphics, grDevices, parallel, tools, mgcv,
MASS, SuppDists, snow
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects.
License: GPL (>= 2)
URL: http://folk.uib.no/gjessing/genetics/software/haplin/
NeedsCompilation: no
Packaged: 2016-05-25 17:09:49 UTC; hkgjess
Repository: CRAN
Date/Publication: 2016-05-26 17:44:32

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'Haplin' ...
** package 'Haplin' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Haplin'
    finding HTML links ... done
    cbindFiles                              html  
    convertPed                              html  
    gwaaToHaplin                            html  
    gxe                                     html  
    hapPower                                html  
    hapRun                                  html  
    hapSim                                  html  
    haplin                                  html  
    haplinSlide                             html  
    haplinStrat                             html  
    haplinTDT                               html  
    haptable                                html  
    lineByLine                              html  
    output                                  html  
    pQQ                                     html  
    pedToHaplin                             html  
    plot.haplin                             html  
    plot.haplinTDT                          html  
    plot.haptable                           html  
    prepPed                                 html  
    print.haplin                            html  
    print.summary.haplin                    html  
    rbindFiles                              html  
Rd warning: /tmp/RtmpuQQNai/R.INSTALL2ac72212602f/Haplin/man/rbindFiles.Rd:26: missing file link 'rbind'
    snpPos                                  html  
    snpPower                                html  
    snpSampleSize                           html  
    suest                                   html  
    summary.haplin                          html  
    summary.haplinTDT                       html  
    toDataFrame                             html  
** building package indices
** testing if installed package can be loaded
* DONE (Haplin)
Making 'packages.html' ... done