subsetSCECols: Subset a SingleCellExperiment object by columns

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Subset a SingleCellExperiment object by columns

Description

Used to peform subsetting of a SingleCellExperiment object using a variety of methods that indicate the correct columns to keep. The various methods, index, bool, and colData, can be used in conjunction with one another.

Usage

subsetSCECols(inSCE, index = NULL, bool = NULL, colData = NULL)

Arguments

inSCE	Input SingleCellExperiment object.
index	Integer vector. Vector of indicies indicating which columns to keep. If NULL, this will not be used for subsetting. Default NULL.
bool	Boolean vector. Vector of TRUE or FALSE indicating which columns should be kept. Needs to be the same length as the number of columns in inSCE. If NULL, this will not be used for subsetting. Default NULL.
colData	Character. An expression that will identify a subset of columns using variables found in the colData of inSCE. For example, if x is a numeric vector in colData, then "x < 5" will return all columns with x less than 5. Single quotes should be used for character strings. For example, "y == 'yes'" will return all columns where y is "yes". Multiple expressions can be evaluated by placing them in a vector. For example c("x < 5", "y =='yes'") will apply both operations for subsetting. If NULL, this will not be used for subsetting. Default NULL.

Value

A SingleCellExperiment object that has been subsetted by colData.

Author(s)

Joshua D. Campbell

Examples

data(scExample)
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.