preprocess: preprocess

In gongx030/scDatasets: Single cell RNA-seq datasets

Description

A function for preprocessing gene expression matrix.

Usage

preprocess(X, min.expressed.gene = 2000, 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 and Il-Youp Kwak

References

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

See Also

DrImpute

Examples

library(scDatasets)
library(SummarizedExperiment)
data(usoskin)
X <- assays(usoskin)$count
X <- preprocess(X, min.expressed.gene = 0)

gongx030/scDatasets documentation built on May 29, 2019, 12:37 p.m.