map_save_ram

Perform map using background objects with only selected markers. It saves ram memory during the procedure.
It is useful if dealing with many markers in total data set.

Analysis of molecular marker data from model (backcrosses,
F2 and recombinant inbred lines) and non-model systems (i. e.
outcrossing species). For the later, it allows statistical
analysis by simultaneously estimating linkage and linkage
phases (genetic map construction) according to Wu et al. (2002)
<doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint
approaches using hidden Markov models.

Cristiane Taniguti

onemap

Construction of Genetic Maps in Experimental Crosses

Gabriel Margarido

Marcelo Mollinari

Getulio Ferreira

Rodrigo Amadeu

Karl Broman

Katharine Preedy

Bastian Schiffthaler

Augusto Garcia

map_save_ram function

<dl><dt>input.seq</dt>
<dd>object of class sequence</dd>
<dt>tol</dt>
<dd>tolerance for the C routine, i.e., the value used to evaluate
convergence.</dd>
<dt>verbose</dt>
<dd>If <code>TRUE</code>, print tracing information.</dd>
<dt>rm_unlinked</dt>
<dd>When some pair of markers do not follow the linkage criteria, 
if <code>TRUE</code> one of the markers is removed and returns a vector with remaining 
marker numbers (useful for mds_onemap and map_avoid_unlinked functions).</dd>
<dt>phase_cores</dt>
<dd>The number of parallel processes to use when estimating
the phase of a marker. (Should be no more than 4)</dd>
<dt>size</dt>
<dd>The center size around which an optimum is to be searched</dd>
<dt>overlap</dt>
<dd>The desired overlap between batches</dd>
<dt>parallelization.type</dt>
<dd>one of the supported cluster types. This should 
be either PSOCK (default) or FORK.</dd>
<dt>max.gap</dt>
<dd>the marker will be removed if it have gaps higher than this defined threshold in both sides</dd></dl>

Arguments

Perform map using background objects with only selected markers. It saves ram memory during the procedure.
It is useful if dealing with many markers in total data set. — map_save_ram

<dl>

<dt>input.seq</dt>
<dd>object of class sequence</dd>


<dt>tol</dt>
<dd>tolerance for the C routine, i.e., the value used to evaluate
convergence.</dd>


<dt>verbose</dt>
<dd>If <code>TRUE</code>, print tracing information.</dd>


<dt>rm_unlinked</dt>
<dd>When some pair of markers do not follow the linkage criteria, 
if <code>TRUE</code> one of the markers is removed and returns a vector with remaining 
marker numbers (useful for mds_onemap and map_avoid_unlinked functions).</dd>


<dt>phase_cores</dt>
<dd>The number of parallel processes to use when estimating
the phase of a marker. (Should be no more than 4)</dd>


<dt>size</dt>
<dd>The center size around which an optimum is to be searched</dd>


<dt>overlap</dt>
<dd>The desired overlap between batches</dd>


<dt>parallelization.type</dt>
<dd>one of the supported cluster types. This should 
be either PSOCK (default) or FORK.</dd>


<dt>max.gap</dt>
<dd>the marker will be removed if it have gaps higher than this defined threshold in both sides</dd>

</dl>

Perform map using background objects with only selected markers. It saves ram memory during the procedure.
It is useful if dealing with many markers in total data set.

map_save_ram: Perform map using background objects with only selected markers. It saves ram memory during the procedure. It is useful if dealing with many markers in total data set.

Description

Usage

Arguments