DrImpute (version 1.0)

preprocessSC: 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

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

# NOT RUN {
data(exdata)
exdata <- preprocessSC(exdata)

# }