objectNormalize

internal

Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.

Yohann Demont

Tools for Imaging Flow Cytometry

Gautier Stoll

Guido Kroemer

Jean-Pierre Marolleau

Loïc Garçon

objectNormalize function

<dl><dt>mat</dt>
<dd>a finite numeric matrix.</dd>
<dt>input_range</dt>
<dd>a finite numeric vector of 2 values, sets the range of the input intensity values. Values outside this range are clipped. Default is <code>[0,4095]</code>.</dd>
<dt>full_range</dt>
<dd>if '<code>full_range</code>' is <code>TRUE</code>, then '<code>input_range</code>' will be set to <code>[0,4095]</code> and '<code>gamma</code>' forced to <code>1</code>. Default is <code>FALSE</code>.</dd>
<dt>force_range</dt>
<dd>if '<code>force_range</code>' is <code>TRUE</code>, then '<code>input_range</code>' will be adjusted to '<code>mat</code>' range in <code>[-4095,+inf]</code> and '<code>gamma</code>' forced to <code>1</code>. Default is <code>FALSE</code>. 
Note that this parameter takes the precedence over <code>input_range</code>' and <code>full_range</code>'.</dd>
<dt>gamma</dt>
<dd>'<code>gamma</code>' correction. Default is <code>1</code>, for no correction.</dd></dl>

Arguments

Object Intensity Normalization — objectNormalize

<dl>

<dt>mat</dt>
<dd>a finite numeric matrix.</dd>


<dt>input_range</dt>
<dd>a finite numeric vector of 2 values, sets the range of the input intensity values. Values outside this range are clipped. Default is <code>[0,4095]</code>.</dd>


<dt>full_range</dt>
<dd>if '<code>full_range</code>' is <code>TRUE</code>, then '<code>input_range</code>' will be set to <code>[0,4095]</code> and '<code>gamma</code>' forced to <code>1</code>. Default is <code>FALSE</code>.</dd>


<dt>force_range</dt>
<dd>if '<code>force_range</code>' is <code>TRUE</code>, then '<code>input_range</code>' will be adjusted to '<code>mat</code>' range in <code>[-4095,+inf]</code> and '<code>gamma</code>' forced to <code>1</code>. Default is <code>FALSE</code>. 
Note that this parameter takes the precedence over <code>input_range</code>' and <code>full_range</code>'.</dd>


<dt>gamma</dt>
<dd>'<code>gamma</code>' correction. Default is <code>1</code>, for no correction.</dd>

</dl>

Object Intensity Normalization

objectNormalize: Object Intensity Normalization

Description

Usage

Value

Arguments

Details