customConvertFeats

Attempt to automatically convert non-ENSEMBL feature identifiers to
ENSEMBL identifiers. Features are included as rownames of the input
data.frame (or matrix). It is assumed that feature identifiers
(i.e., rownames of x) come from human or mouse genomes, and
are either OFFICIAL SYMBOLS or ENTREZIDS. If less than 20
is identified, an error will be thrown.

An open, multi-algorithmic pipeline for easy, fast and efficient
analysis of cellular sub-populations and the molecular signatures that
characterize them. The pipeline consists of four successive steps: data
pre-processing, cellular clustering with pseudo-temporal ordering, defining
differential expressed genes and biomarker identification. More details on
Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements
extensions of the work published by Ghannoum et. al. (2019)
<doi:10.1101/700989>.

Waldir Leoncio

DIscBIO

A User-Friendly Pipeline for Biomarker Discovery in Single-Cell
Transcriptomics

Salim Ghannoum

Alvaro Köhn-Luque

Damiano Fantini

customConvertFeats function

<dl><dt>x</dt>
<dd>data.frame or matrix including raw counts (typically, UMIs),
where rows are features (genes) and rownames are feature identifiers
(SYMBOLs or ENTREZIDs).</dd>
<dt>verbose</dt>
<dd>logical, shall messages be printed to inform about
conversion advances.</dd></dl>

Arguments

Automatic Feature Id Conversion. — customConvertFeats

<dl>

<dt>x</dt>
<dd>data.frame or matrix including raw counts (typically, UMIs),
where rows are features (genes) and rownames are feature identifiers
(SYMBOLs or ENTREZIDs).</dd>


<dt>verbose</dt>
<dd>logical, shall messages be printed to inform about
conversion advances.</dd>

</dl>

customConvertFeats: Automatic Feature Id Conversion.

Description

Usage

Value

Arguments