setContaminationFraction

Manually specify the contamination fraction.

Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) <doi:10.1101/303727>.

Matthew Young

SoupX

Single Cell mRNA Soup eXterminator

setContaminationFraction function

<dl><dt>sc</dt>
<dd>A SoupChannel object.</dd>
<dt>contFrac</dt>
<dd>The contamination fraction. Either a constant, in which case the same value is used for all cells, or a named vector, in which case the value is set for each cell.</dd>
<dt>forceAccept</dt>
<dd>A warning or error is usually returned for extremely high contamination fractions. Setting this to TRUE will turn these into messages and proceed.</dd></dl>

Arguments

Manually set contamination fraction — setContaminationFraction

<dl>

<dt>sc</dt>
<dd>A SoupChannel object.</dd>


<dt>contFrac</dt>
<dd>The contamination fraction. Either a constant, in which case the same value is used for all cells, or a named vector, in which case the value is set for each cell.</dd>


<dt>forceAccept</dt>
<dd>A warning or error is usually returned for extremely high contamination fractions. Setting this to TRUE will turn these into messages and proceed.</dd>

</dl>

setContaminationFraction: Manually set contamination fraction

Description

Usage

Value

Arguments

Examples