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
Examples
data(exdata)
exdata <- preprocessSC(exdata)
[Package DrImpute version 1.0 Index]