preprocessSC {DrImpute}

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)