remove.TRAMP.match

Key of sample and known, respectively.
 See <code><a rd-options="" href="/link/TRAMPsamples?package=TRAMPR&version=1.0-10" data-mini-rdoc="TRAMPR::TRAMPsamples">TRAMPsamples</a></code> and <code><a rd-options="" href="/link/TRAMPknowns?package=TRAMPR&version=1.0-10" data-mini-rdoc="TRAMPR::TRAMPknowns">TRAMPknowns</a></code> for
 more information.

sample.fk, knowns.fk

Mark a match in a TRAMP object as ignored; when this is
 set, a match will be ignored when producing presence/absence matrices
 (see <code><a rd-options="" href="/link/summary.TRAMP?package=TRAMPR&version=1.0-10" data-mini-rdoc="TRAMPR::summary.TRAMP">summary.TRAMP</a></code>) or when plotting
 (<code><a rd-options="" href="/link/plot.TRAMP?package=TRAMPR&version=1.0-10" data-mini-rdoc="TRAMPR::plot.TRAMP">plot.TRAMP</a></code>) when <code>ignore</code> is <code>TRUE</code>.
 <code><a rd-options="" href="/link/update.TRAMP?package=TRAMPR&version=1.0-10" data-mini-rdoc="TRAMPR::update.TRAMP">update.TRAMP</a></code> provides an interactive interface for doing
 this, but <code>remove.TRAMP.match</code> may be useful directly.

manip

Matching terminal restriction fragment length
polymorphism ('TRFLP') profiles between unknown samples and a
database of known samples.  'TRAMPR' facilitates analysis of
many unknown profiles at once, and provides tools for working
directly with electrophoresis output through to generating
summaries suitable for community analyses with R's rich set of
statistical functions.  'TRAMPR' also resolves the issues of
multiple 'TRFLP' profiles within a species, and shared 'TRFLP'
profiles across species.

Rich FitzJohn

TRAMPR

'TRFLP' Analysis and Matching Package for R

Ian Dickie

remove.TRAMP.match function

This should be regarded as experimental. There is currently no
 mechanism for restoring ignored matches, aside from recreating the
 <code>TRAMP</code> object, or through editing <code>x$presence.ign</code> directly
 (the format of that table is self-explanatory, but is not guaranteed
 not to change between TRAMP versions). Note that by default,
 <code><a rd-options="" href="/link/summary.TRAMP?package=TRAMPR&version=1.0-10" data-mini-rdoc="TRAMPR::summary.TRAMP">summary.TRAMP</a></code> and <code><a rd-options="" href="/link/plot.TRAMP?package=TRAMPR&version=1.0-10" data-mini-rdoc="TRAMPR::plot.TRAMP">plot.TRAMP</a></code> will not
 remove matches; you must specify <code>ignore=TRUE</code> to enable this.

Warning

Key of sample and known, respectively.
 See <code><a rd-options='' href='TRAMPsamples'>TRAMPsamples</a></code> and <code><a rd-options='' href='TRAMPknowns'>TRAMPknowns</a></code> for
 more information.

Mark a match in a TRAMP object as ignored; when this is
 set, a match will be ignored when producing presence/absence matrices
 (see <code><a rd-options='' href='summary.TRAMP'>summary.TRAMP</a></code>) or when plotting
 (<code><a rd-options='' href='plot.TRAMP'>plot.TRAMP</a></code>) when <code>ignore</code> is <code>TRUE</code>.
 <code><a rd-options='' href='update.TRAMP'>update.TRAMP</a></code> provides an interactive interface for doing
 this, but <code>remove.TRAMP.match</code> may be useful directly.

Mark a TRAMP Match as Ignored — remove.TRAMP.match

This should be regarded as experimental. There is currently no
 mechanism for restoring ignored matches, aside from recreating the
 <code>TRAMP</code> object, or through editing <code>x$presence.ign</code> directly
 (the format of that table is self-explanatory, but is not guaranteed
 not to change between TRAMP versions). Note that by default,
 <code><a rd-options='' href='summary.TRAMP'>summary.TRAMP</a></code> and <code><a rd-options='' href='plot.TRAMP'>plot.TRAMP</a></code> will not
 remove matches; you must specify <code>ignore=TRUE</code> to enable this.

remove.TRAMP.match: Mark a TRAMP Match as Ignored

Description

Usage

Arguments

Value

Warning