setDR

Manually specify the dimension reduction

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

setDR function

<dl><dt>sc</dt>
<dd>A SoupChannel object.</dd>
<dt>DR</dt>
<dd>The dimension reduction coordinates (e.g., tSNE). This must be a data.frame, with two columns giving the two dimension reduction coordinates. The data.frame must either have row names matching the row names of sc$metaData, or be ordered in the same order as sc$metaData.</dd>
<dt>reductName</dt>
<dd>What to name the reduction (defaults to column names provided).</dd></dl>

Arguments

Manually set dimension reduction for a channel — setDR

<dl>

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


<dt>DR</dt>
<dd>The dimension reduction coordinates (e.g., tSNE). This must be a data.frame, with two columns giving the two dimension reduction coordinates. The data.frame must either have row names matching the row names of sc$metaData, or be ordered in the same order as sc$metaData.</dd>


<dt>reductName</dt>
<dd>What to name the reduction (defaults to column names provided).</dd>

</dl>

setDR: Manually set dimension reduction for a channel

Description

Usage

Value

Arguments

Examples