filter_counts: filter_counts

In Malindrie/scShapes: A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data

filter_counts

Description

This function is used to preprocess matrix of read counts to only keep genes with a certain number of nonzero entries.

Usage

filter_counts(counts, perc.zero = 0.1)

Arguments

counts	A non-negative integer matrix of scRNA-seq raw read counts. The rows of the matrix are genes and columns are samples/cells.
perc.zero	A numeric value between 0 and 1 that represents the proportion of zeros per gene in the processed dataset.

Value

An object of class Matrix with genes removed if they have more than perc.zero zeros.

Examples

# load toy  example data

data(scData)

# apply the filter_counts function to filter out genes if they have
# more than 10% zero

scData_filt <- filter_counts(scData$counts, perc.zero = 0.1)

Malindrie/scShapes documentation built on Nov. 21, 2022, 8:58 a.m.