read.haplo.shapeit_haps

character, path to a <code>.haps</code> file containing
haplotype data which is regular ShapeIt output. See
<a href="https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#hapsample">https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#hapsample</a>

filename

object, data.frame contains 3 columns: rsID, chromosome,
position in bp as output by e.g. <code><a rd-options="" href="/link/readMapFile?package=RVPedigree&version=0.0.3" data-mini-rdoc="RVPedigree::readMapFile">readMapFile</a></code>.

character, chromosome number (basically from 1 to 22 as used by
<a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped">Plink</a>),
on which the region of interest is located

numeric, start position (in bp, base pairs) of the
region of interest (default: 0)

startpos

numeric, end position (in bp, base pairs) of the
region of interest (default: 0)

endpos


Read haplotype data, selected by region of interest, from a .haps file
(regular ShapeIt output files)


internal

This is a collection of the five region-based
rare-variant genetic association tests. The following tests are
currently implemented: ASKAT, ASKAT-Normalized, VC-C1, VC-C2 and
VC-C3.

read.haplo.shapeit_haps: Read haplotype data, selected by region of interest, from a .haps file (regular ShapeIt output files)

Description

Usage

Arguments

Value

See Also