run_pipeline

Run the main pipeline for ScRNAIMM

Performing single-cell imputation in a way that preserves the biological variations in the data. The package clusters the input data to do imputation for each cluster, and do a distribution check using the Anderson-Darling normality test to impute dropouts using mean or median (Yazici, B., & Yolacan, S. (2007) <DOI:10.1080/10629360600678310>).

Mohamed Soudy

ScRNAIMM

Performing Single-Cell RNA-Seq Imputation by Using Mean/Median
Imputation

Sascha Jung

Antonio DEL SOL

run_pipeline function

<dl><dt>ScRNA</dt>
<dd>ScRNA-seq data set generated by prepare_dataset function</dd>
<dt>label</dt>
<dd>Prior knowledge about cluster labels if NULL, will use our clustering function</dd>
<dt>k</dt>
<dd>Prior knowledge about number of clusters if NULL, will use our clustering function</dd>
<dt>cells</dt>
<dd>Boolean whether to do the imputation based on cell clustering or not</dd>
<dt>genes</dt>
<dd>Boolean whether to do the imputation based on genes or not</dd>
<dt>outdir</dt>
<dd>Path to output directory to write the imputed data</dd>
<dt>dataset</dt>
<dd>Name of the data set to be the name of the output directory</dd></dl>

Arguments

Mohamed Soudy <a href="/link/Mohmedsoudy2009%40gmail.com?package=ScRNAIMM&version=0.1" data-mini-rdoc="ScRNAIMM::Mohmedsoudy2009@gmail.com">Mohmedsoudy2009@gmail.com</a>

Author

Run the main pipeline for ScRNAIMM — run_pipeline

<dl>

<dt>ScRNA</dt>
<dd>ScRNA-seq data set generated by prepare_dataset function</dd>


<dt>label</dt>
<dd>Prior knowledge about cluster labels if NULL, will use our clustering function</dd>


<dt>k</dt>
<dd>Prior knowledge about number of clusters if NULL, will use our clustering function</dd>


<dt>cells</dt>
<dd>Boolean whether to do the imputation based on cell clustering or not</dd>


<dt>genes</dt>
<dd>Boolean whether to do the imputation based on genes or not</dd>


<dt>outdir</dt>
<dd>Path to output directory to write the imputed data</dd>


<dt>dataset</dt>
<dd>Name of the data set to be the name of the output directory</dd>

</dl>

Mohamed Soudy <a href='mailto:Mohmedsoudy2009@gmail.com'>Mohmedsoudy2009@gmail.com</a>

run_pipeline: Run the main pipeline for ScRNAIMM

Description

Usage

Value

Arguments

Author