IBDhaploRtools: Functions for the Analysis of IBD Haplo Output.

Functions to analyze, plot, and store the output of running IBD_Haplo software package. More information regarding IBD_Haplo can be found at http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml.

Author
Marshall Brown, Fiona Grimson
Date of publication
2015-02-14 01:16:14
Maintainer
Fiona Grimson <fgrimson@uw.edu>
License
GPL-3
Version
1.8

View on R-Forge

Man pages

cumul.sum
cumulative.sums
get.counts
get counts
h.to.g
Convert haplotype states to genotype states
ibdhap.barplot
create ibd barplot
ibdhap.compare.loci
ibdhap compare.loci
ibdhap.compare.segs
ibdhap compare segments
IBDhaploRtools-package
Functions for the Analysis of IBD Haplo output
ibdhap.make.calls
ibdhap.make.calls
ibdhap.make.true
ibdhap make true states
ibdhap.names
Get chromosome names
ibdhap.reduce.states
ibdhap reduce states
ibdhap.seg.lengths
ibdhap.seg.lengths
ibdhap.summary
ibdhap summary of called states
ibdhap.transitions
create transition matrix
ids_phased
Example MORGAN IBDhaplo output
make.col.vec
make color vector
meet.cutoff
meet cutoff
removezeros
remove zeros
return.ibd.val
return ibd value
sumcol
sum over specific columns

Files in this package

IBDhaploRtools/DESCRIPTION
IBDhaploRtools/NAMESPACE
IBDhaploRtools/R
IBDhaploRtools/R/cumul.sum.R
IBDhaploRtools/R/get.counts.R
IBDhaploRtools/R/h.to.g.R
IBDhaploRtools/R/ibdhap.barplot.R
IBDhaploRtools/R/ibdhap.compare.loci.R
IBDhaploRtools/R/ibdhap.compare.segs.R
IBDhaploRtools/R/ibdhap.make.calls.R
IBDhaploRtools/R/ibdhap.make.true.R
IBDhaploRtools/R/ibdhap.names.R
IBDhaploRtools/R/ibdhap.reduce.states.R
IBDhaploRtools/R/ibdhap.seg.lengths.R
IBDhaploRtools/R/ibdhap.summary.calls.R
IBDhaploRtools/R/ibdhap.transitions.R
IBDhaploRtools/R/make.col.vec.R
IBDhaploRtools/R/meet.cutoff.R
IBDhaploRtools/R/removezeros.R
IBDhaploRtools/R/return.ibd.val.R
IBDhaploRtools/R/sumcol.R
IBDhaploRtools/build
IBDhaploRtools/build/vignette.rds
IBDhaploRtools/data
IBDhaploRtools/data/ids_phased.RData
IBDhaploRtools/data/ids_unphased.RData
IBDhaploRtools/data/posvec.RData
IBDhaploRtools/data/qibd_phased.RData
IBDhaploRtools/data/qibd_unphased.RData
IBDhaploRtools/data/trueibd_phased.RData
IBDhaploRtools/inst
IBDhaploRtools/inst/doc
IBDhaploRtools/inst/doc/IBDhaploRtools_tutorial.R
IBDhaploRtools/inst/doc/IBDhaploRtools_tutorial.Rnw
IBDhaploRtools/inst/doc/IBDhaploRtools_tutorial.pdf
IBDhaploRtools/man
IBDhaploRtools/man/IBDhaploRtools-package.Rd
IBDhaploRtools/man/cumul.sum.Rd
IBDhaploRtools/man/get.counts.Rd
IBDhaploRtools/man/h.to.g.Rd
IBDhaploRtools/man/ibdhap.barplot.Rd
IBDhaploRtools/man/ibdhap.compare.loci.Rd
IBDhaploRtools/man/ibdhap.compare.segs.Rd
IBDhaploRtools/man/ibdhap.make.calls.Rd
IBDhaploRtools/man/ibdhap.make.true.Rd
IBDhaploRtools/man/ibdhap.names.Rd
IBDhaploRtools/man/ibdhap.reduce.states.Rd
IBDhaploRtools/man/ibdhap.seg.lengths.Rd
IBDhaploRtools/man/ibdhap.summary.Rd
IBDhaploRtools/man/ibdhap.transitions.Rd
IBDhaploRtools/man/ids_phased.Rd
IBDhaploRtools/man/make.col.vec.Rd
IBDhaploRtools/man/meet.cutoff.Rd
IBDhaploRtools/man/removezeros.Rd
IBDhaploRtools/man/return.ibd.val.Rd
IBDhaploRtools/man/sumcol.Rd
IBDhaploRtools/vignettes
IBDhaploRtools/vignettes/IBDhaploRtools_tutorial.Rnw