R: A function for preprocessing gene expression matrix.

preprocessSC {DrImpute} | R Documentation

## A function for preprocessing gene expression matrix.

### Description

Preprocess gene expression data

### Usage

    preprocessSC(X, min.expressed.gene = 0, min.expressed.cell = 2,
      max.expressed.ratio = 1, normalize.by.size.effect = FALSE)

### Arguments

`X` | Gene expression matrix (Gene by Cell).
`min.expressed.gene` | Cell level filtering criteria. For a given cell, if the number of expressed genes are less than min.expressed.gene, we filter it out.
`min.expressed.cell` | Gene level filtering criteria. For a given gene, if the number of expressed cells are less than min.expressed.cell, we filter it out.
`max.expressed.ratio` | Gene level filtering criteria. For a given gene, if the ratio of expressed cells are larger than max.expressed.ratio, we filter it out.
`normalize.by.size.effect` | Normaize using size factor.

### Value

Filtered gene expression matrix

### Author(s)

Wuming Gong

### References

Il-Youp Kwak, Wuming Gong, Kaoko Koyano-Nakagawa and Daniel J. Garry (2017+) DrImpute: Imputing dropout eveents in single cell RNA sequencing data

### See Also

`DrImpute`

### Examples

    data(exdata)
    exdata <- preprocessSC(exdata)

[Package DrImpute version 1.0 Index]