read10xMatrix

This function reads a matrix generated by the 10x processing pipeline
from the specified directory and returns it. It aborts if one of the required
files in the specified directory do not exist.

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

read10xMatrix function

<dl><dt>path</dt>
<dd>string Location of 10x output</dd>
<dt>version</dt>
<dd>string Version of 10x output to read (default='V3'). Must be one of 'V2' or 'V3'.</dd>
<dt>transcript.id</dt>
<dd>string Transcript identifier to use (default='SYMBOL'). Must be either 'SYMBOL' (e.g. "Sox17") or 'ENSEMBL' (e.g. "ENSMUSG00000025902"). This value is case-sensitive.</dd>
<dt>verbose</dt>
<dd>boolean Whether to return verbose output</dd></dl>

Arguments

This function reads a matrix generated by the 10x processing pipeline
from the specified directory and returns it. It aborts if one of the required
files in the specified directory do not exist. — read10xMatrix

<dl>

<dt>path</dt>
<dd>string Location of 10x output</dd>


<dt>version</dt>
<dd>string Version of 10x output to read (default='V3'). Must be one of 'V2' or 'V3'.</dd>


<dt>transcript.id</dt>
<dd>string Transcript identifier to use (default='SYMBOL'). Must be either 'SYMBOL' (e.g. "Sox17") or 'ENSEMBL' (e.g. "ENSMUSG00000025902"). This value is case-sensitive.</dd>


<dt>verbose</dt>
<dd>boolean Whether to return verbose output</dd>

</dl>

This function reads a matrix generated by the 10x processing pipeline
from the specified directory and returns it. It aborts if one of the required
files in the specified directory do not exist.

read10xMatrix: This function reads a matrix generated by the 10x processing pipeline from the specified directory and returns it. It aborts if one of the required files in the specified directory do not exist.

Description

Usage

Value

Arguments