data_rm_pops

Removes populations from an already existing `IFC_data` object.

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

data_rm_pops function

<dl><dt>obj</dt>
<dd>an `IFC_data` object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).</dd>
<dt>pops</dt>
<dd>a character vector of population names to remove within 'obj'. Note that "All" and "" are not allowed and will be excluded from 'pops' if present.</dd>
<dt>list_only</dt>
<dd>whether to return a list of elements that will be impacted by the removal. Default is TRUE.
If FALSE then modified object will be returned.</dd>
<dt>adjust_graph</dt>
<dd>whether to try to adjust graph(s) when possible. Default is TRUE. 
-TRUE, graph(s) will be kept if possible using only regions, pops it depends that can be found in 'obj', 
-FALSE, graph(s) will be kept only if all features, regions, pops it refers to are found in 'obj', 
-NA, graph(s) will be removed no matter if features, regions, pops it refers to are found in 'obj'.</dd>
<dt>...</dt>
<dd>Other arguments to be passed.</dd></dl>

Arguments

Remove Population from an IFC_data Object — data_rm_pops

<dl>

<dt>obj</dt>
<dd>an `IFC_data` object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).</dd>


<dt>pops</dt>
<dd>a character vector of population names to remove within 'obj'. Note that "All" and "" are not allowed and will be excluded from 'pops' if present.</dd>


<dt>list_only</dt>
<dd>whether to return a list of elements that will be impacted by the removal. Default is TRUE.
If FALSE then modified object will be returned.</dd>


<dt>adjust_graph</dt>
<dd>whether to try to adjust graph(s) when possible. Default is TRUE. 
-TRUE, graph(s) will be kept if possible using only regions, pops it depends that can be found in 'obj', 
-FALSE, graph(s) will be kept only if all features, regions, pops it refers to are found in 'obj', 
-NA, graph(s) will be removed no matter if features, regions, pops it refers to are found in 'obj'.</dd>


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

</dl>

data_rm_pops: Remove Population from an IFC_data Object

Description

Usage

Value

Arguments