redefine_masks

Helper to 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_masks function

<dl><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>new_images_names</dt>
<dd>a vector of image name to use for replacing 'images' names. Default is images$name</dd>
<dt>to_match_mask</dt>
<dd>a string with a mask name to use for matching 'masks' names. Default is NULL</dd>
<dt>to_replace_mask</dt>
<dd>a string of mask name to use for replacing 'masks' names. Default is NULL</dd>
<dt>...</dt>
<dd>Other arguments to be passed.</dd></dl>

Arguments

IFC_masks Redefinition — redefine_masks

<dl>

<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>new_images_names</dt>
<dd>a vector of image name to use for replacing 'images' names. Default is images$name</dd>


<dt>to_match_mask</dt>
<dd>a string with a mask name to use for matching 'masks' names. Default is NULL</dd>


<dt>to_replace_mask</dt>
<dd>a string of mask name to use for replacing 'masks' names. Default is NULL</dd>


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

</dl>

redefine_masks: IFC_masks Redefinition

Description

Usage

Value

Arguments