readDatfile

Converts dat files in LINKAGE format to dat/map/freq files in MERLIN format

NOTE: 'PARAMLINK' HAS BEEN SUPERSEDED BY THE 'PEDSUITE'
PACKAGES (<https://magnusdv.github.io/pedsuite/>). 'PARAMLINK' IS
MAINTAINED ONLY FOR LEGACY PURPOSES AND SHOULD NOT BE USED IN NEW
PROJECTS. A suite of tools for analysing pedigrees with marker data,
including parametric linkage analysis, forensic computations,
relatedness analysis and marker simulations. The core of the package
is an implementation of the Elston-Stewart algorithm for pedigree
likelihoods, extended to allow mutations as well as complex
inbreeding. Features for linkage analysis include singlepoint LOD
scores, power analysis, and multipoint analysis (the latter through a
wrapper to the 'MERLIN' software). Forensic applications include
exclusion probabilities, genotype distributions and conditional
simulations. Data from the 'Familias' software can be imported and
analysed in 'paramlink'. Finally, 'paramlink' offers many utility
functions for creating, manipulating and plotting pedigrees with or
without marker data (the actual plotting is done by the 'kinship2'
package).

Magnus Vigeland

paramlink

Parametric Linkage and Other Pedigree Analysis in R

Magnus Dehli Vigeland

Thore Egeland

Guro Doerum

readDatfile function

<dl><dt>datfile</dt>
<dd>character. The path to the dat file.</dd>
<dt>chrom</dt>
<dd>integer chromosome number (needed to create the MERLIN map).</dd>
<dt>comment_string</dt>
<dd>character indicating comments (which are removed before
processing).</dd>
<dt>write_to</dt>
<dd>a character prefix used for naming the output files, or NULL
if no files should be written.</dd></dl>

Arguments

Read dat file in LINKAGE format — readDatfile

<dl>

<dt>datfile</dt>
<dd>character. The path to the dat file.</dd>


<dt>chrom</dt>
<dd>integer chromosome number (needed to create the MERLIN map).</dd>


<dt>comment_string</dt>
<dd>character indicating comments (which are removed before
processing).</dd>


<dt>write_to</dt>
<dd>a character prefix used for naming the output files, or NULL
if no files should be written.</dd>

</dl>

readDatfile: Read dat file in LINKAGE format

Description

Usage

Value

Arguments

Examples