cvCalcBulkProfile

This function allows to calculate Intra-donor variations in bulk data over
longitudinal timepoints and visualize in a CV vs Mean plot. Plots stored in
output directory.

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

cvCalcBulkProfile function

<dl><dt>data_object</dt>
<dd>Input PALMO S4 object. It contains annotation
information and expression data from Bulk or single cell data.</dd>
<dt>cl</dt>
<dd>Number of clusters. Use nCores-1 to run parallel. Default 2</dd>
<dt>fileName</dt>
<dd>User-defined filename, Default outputFile</dd>
<dt>filePATH</dt>
<dd>User-defined output directory PATH Default, current
directory</dd></dl>

Arguments

cvCalcBulkProfile Function — cvCalcBulkProfile

<dl>

<dt>data_object</dt>
<dd>Input PALMO S4 object. It contains annotation
information and expression data from Bulk or single cell data.</dd>


<dt>cl</dt>
<dd>Number of clusters. Use nCores-1 to run parallel. Default 2</dd>


<dt>fileName</dt>
<dd>User-defined filename, Default outputFile</dd>


<dt>filePATH</dt>
<dd>User-defined output directory PATH Default, current
directory</dd>

</dl>

cvCalcBulkProfile: cvCalcBulkProfile Function

Description

Usage

Value

Arguments

Examples