createPALMOobject

This function allows to create PALMO object using Annotation dataframe and
Data dataframe. The Data can be bulk data or single cell data. The bulk input
data should consists of rows as genes/proteins/features and column as Sample
name (same as user-defined Samples in Annotation dataframe). The single cell
data should be Seurat object (please check
https://search.r-project.org/CRAN/refmans/SeuratObject/html/CreateSeuratObject.html).
In case Seurat object not available then user can use function
createPALMOfromsinglecellmatrix to create PALMO object. The Seurat
object/metadata should have Sample column corresponding to Annotation
dataframe.

It is a platform for analyzing longitudinal data from bulk as well as single cell datasets. It allows to identify variations in molecular features within and across donors over longitudinal time points. The analysis can be done on bulk expression dataset without known cell type information or single cell with cell type/user-defined groups. It allows to infer stable and variable features in given donor and each cell type (or user defined group). The outlier analysis can be performed to identify technical/biological perturbed samples in donor/participant. Further, differential analysis can be performed to decipher time-wise changes in gene expression in a cell type.

Suhas Vasaikar

PALMO

Identify Intra and Inter-Donor Variations in Bulk or Single Cell
Longitudinal Dataset

Aarthi Talla

Xiaojun Li

createPALMOobject function

<dl><dt>anndata</dt>
<dd>Annotation dataframe. It consist of information such as
Sample (sample name), PTID (donor/participant), Time
(longitudinal timepoints)</dd>
<dt>data</dt>
<dd>Data can be bulk data or single cell data</dd></dl>

Arguments

createPALMOobject Function — createPALMOobject

<dl>

<dt>anndata</dt>
<dd>Annotation dataframe. It consist of information such as
Sample (sample name), PTID (donor/participant), Time
(longitudinal timepoints)</dd>


<dt>data</dt>
<dd>Data can be bulk data or single cell data</dd>

</dl>

createPALMOobject: createPALMOobject Function

Description

Usage

Value

Arguments

Examples