randCyto

A sample dataset containing information about flow cytometry data with two binary conditions and four markers. The data are a random subset of the 'extdata' data in the 'flowWorkspaceData' package found on Bioconductor <a href="https://bioconductor.org/packages/release/data/experiment/html/flowWorkspaceData.html">https://bioconductor.org/packages/release/data/experiment/html/flowWorkspaceData.html</a> and formatted for 'gateR' input. The selected markers are arcsinh transformed.

datasets

Estimates statistically significant marker combination values within
which one immunologically distinctive group (i.e., disease case) is more associated than
another group (i.e., healthy control), successively, using various combinations (i.e.,
"gates") of markers to examine features of cells that may be different between
groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk
function estimated using the 'sparr' package. Details about the 'sparr' package
methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details
about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>.
More information about relative risk functions using kernel density estimation can be
found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.

Ian D. Buller

gateR

Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

Elena Hsieh

Debashis Ghosh

Lance A. Waller

NCI 

randCyto function

A data frame with 11763 rows and 7 variables:<dl>
<dt>id</dt>
<dd>cell ID number</dd><dt>g1</dt>
<dd>binary condition #1</dd><dt>g2</dt>
<dd>binary condition #2</dd><dt>arcsinh_CD4</dt>
<dd>arcsinh-transformed CD4</dd><dt>arcsinh_CD38</dt>
<dd>arcsinh-transformed CD38</dd><dt>arcsinh_CD8</dt>
<dd>arcsinh-transformed CD8</dd><dt>arcsinh_CD3</dt>
<dd>arcsinh-transformed CD3</dd>
</dl>

Format

A sample dataset containing information about flow cytometry data with two binary conditions and four markers. The data are a random subset of the 'extdata' data in the 'flowWorkspaceData' package found on Bioconductor <a href='https://bioconductor.org/packages/release/data/experiment/html/flowWorkspaceData.html'>https://bioconductor.org/packages/release/data/experiment/html/flowWorkspaceData.html</a> and formatted for 'gateR' input. The selected markers are arcsinh transformed.

Subset of the 'extdata' data in the 'flowWorkspaceData' package — randCyto

A data frame with 11763 rows and 7 variables:<dl>
<dt>id</dt>
<dd>cell ID number</dd>

<dt>g1</dt>
<dd>binary condition #1</dd>

<dt>g2</dt>
<dd>binary condition #2</dd>

<dt>arcsinh_CD4</dt>
<dd>arcsinh-transformed CD4</dd>

<dt>arcsinh_CD38</dt>
<dd>arcsinh-transformed CD38</dd>

<dt>arcsinh_CD8</dt>
<dd>arcsinh-transformed CD8</dd>

<dt>arcsinh_CD3</dt>
<dd>arcsinh-transformed CD3</dd>


</dl>

randCyto: Subset of the 'extdata' data in the 'flowWorkspaceData' package

Description

Usage

Arguments

Format

Examples