redefine_features_def

Helper modify features_def according to masks or images redefinition.

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

redefine_features_def function

<dl><dt>features_def</dt>
<dd>an `IFC_features_def` object, or a list containing features definition. Default is missing.</dd>
<dt>masks</dt>
<dd>an `IFC_masks` object or a data.frame containing masks definition and name. Default is missing.</dd>
<dt>images</dt>
<dd>a data.frame containing images definition. Default is missing.</dd>
<dt>to_match_feat</dt>
<dd>a string with a features_def name to use for matching 'features_def' names. Default is NULL</dd>
<dt>to_replace_feat</dt>
<dd>a string of features_def name to use for replacing 'features_def' names. Default is NULL</dd>
<dt>...</dt>
<dd>Other arguments to be passed.</dd></dl>

Arguments

IFC_features_def Redefinition — redefine_features_def

<dl>

<dt>features_def</dt>
<dd>an `IFC_features_def` object, or a list containing features definition. Default is missing.</dd>


<dt>masks</dt>
<dd>an `IFC_masks` object or a data.frame containing masks definition and name. Default is missing.</dd>


<dt>images</dt>
<dd>a data.frame containing images definition. Default is missing.</dd>


<dt>to_match_feat</dt>
<dd>a string with a features_def name to use for matching 'features_def' names. Default is NULL</dd>


<dt>to_replace_feat</dt>
<dd>a string of features_def name to use for replacing 'features_def' names. Default is NULL</dd>


<dt>...</dt>
<dd>Other arguments to be passed.</dd>

</dl>

redefine_features_def: IFC_features_def Redefinition

Description

Usage

Value

Arguments