buildMask

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

buildMask 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>definition</dt>
<dd>whether to compute masks definition or masks names. Default is TRUE, to compute definition.</dd>
<dt>to_match_mask</dt>
<dd>a vector of masks names to use for matching 'masks' names. Default is NULL</dd>
<dt>to_replace_mask</dt>
<dd>a vector of masks names to use for replacing 'masks' names. Default is NULL</dd>
<dt>to_match_image</dt>
<dd>a vector of images names to use for matching 'images' names. Default is NULL</dd>
<dt>to_replace_image</dt>
<dd>a vector of images names to use for replacing 'images' names. Default is NULL</dd>
<dt>...</dt>
<dd>Other arguments to be passed.</dd></dl>

Arguments

IFC Mask Coercion — buildMask

<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>definition</dt>
<dd>whether to compute masks definition or masks names. Default is TRUE, to compute definition.</dd>


<dt>to_match_mask</dt>
<dd>a vector of masks names to use for matching 'masks' names. Default is NULL</dd>


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


<dt>to_match_image</dt>
<dd>a vector of images names to use for matching 'images' names. Default is NULL</dd>


<dt>to_replace_image</dt>
<dd>a vector of images names to use for replacing 'images' names. Default is NULL</dd>


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

</dl>

IFC Mask Coercion

buildMask: IFC Mask Coercion

Description

Usage

Value

Arguments

Details