factorFromP2Selection

Returns a factor of cell membership from a p2 selection object
the factor only includes cells present in the selection. If the selection
contains multiclassified cells an error is raised

Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.

Evan Biederstedt

pagoda2

Single Cell Analysis and Differential Expression

Nikolas Barkas

Viktor Petukhov

Peter Kharchenko

Simon Steiger

Rasmus Rydbirk

factorFromP2Selection function

<dl><dt>sel</dt>
<dd>a pagoda2 selection as genereated by readPagoda2SelectionFile</dd>
<dt>use.internal.name</dt>
<dd>boolean Whether to use field 'internal.name' as factor names (default=FALSE)</dd>
<dt>flatten</dt>
<dd>boolean Whether to ignore multiclassified cells, overwriting randomly (default=FALSE)</dd></dl>

Arguments

Returns a factor of cell membership from a p2 selection object
the factor only includes cells present in the selection. If the selection
contains multiclassified cells an error is raised — factorFromP2Selection

<dl>

<dt>sel</dt>
<dd>a pagoda2 selection as genereated by readPagoda2SelectionFile</dd>


<dt>use.internal.name</dt>
<dd>boolean Whether to use field 'internal.name' as factor names (default=FALSE)</dd>


<dt>flatten</dt>
<dd>boolean Whether to ignore multiclassified cells, overwriting randomly (default=FALSE)</dd>

</dl>

Returns a factor of cell membership from a p2 selection object
the factor only includes cells present in the selection. If the selection
contains multiclassified cells an error is raised

factorFromP2Selection: Returns a factor of cell membership from a p2 selection object the factor only includes cells present in the selection. If the selection contains multiclassified cells an error is raised

Description

Usage

Value

Arguments