check_outliers

Add or update <code>"is_outlier"</code> column in the <code>"nacho"</code> field of an object from
a call to <code>load_rcc()</code> or <code>normalise()</code> (<code>nacho_object$nacho</code>),
using the current quality-control thresholds.

NanoString nCounter data are gene expression assays
where there is no need for the use of enzymes or amplification
protocols and work with fluorescent barcodes (Geiss et al. (2018)
<doi:10.1038/nbt1385>). Each barcode is assigned a
messenger-RNA/micro-RNA (mRNA/miRNA) which after bonding with its
target can be counted. As a result each count of a specific barcode
represents the presence of its target mRNA/miRNA. 'NACHO' (NAnoString
quality Control dasHbOard) is able to analyse the exported NanoString
nCounter data and facilitates the user in performing a quality
control. 'NACHO' does this by visualising quality control metrics,
expression of control genes, principal components and sample specific
size factors in an interactive web application.

Mickaël Canouil

NACHO

NanoString Quality Control Dashboard

Roderick Slieker

Gerard Bouland

check_outliers function

<dl><dt>nacho_object</dt>
<dd>[<a href="/link/list?package=NACHO&version=2.0.6" data-mini-rdoc="NACHO::list">list</a>] A list object of class <code>"nacho"</code> obtained
from <code>load_rcc()</code> or <code>normalise()</code>.</dd></dl>

Arguments

Annotate a "nacho" object for outliers — check_outliers

<dl>

<dt>nacho_object</dt>
<dd>[<a href='https://rdrr.io/r/base/list.html'>list</a>] A list object of class <code>"nacho"</code> obtained
from <code>load_rcc()</code> or <code>normalise()</code>.</dd>

</dl>

check_outliers: Annotate a "nacho" object for outliers

Description

Usage

Value

Arguments

Examples