whichCells: Which cells

In farrellja/URD: URD

Description

Identifies cells that meet particular criteria and returns their cell names. This can be used to select populations for subsetting, differential expression, plotting, etc.

Usage

whichCells(object, label, value, label.type = "search")

Arguments

object	An URD object
label	(Character) The label of the data to search for
value	(Character or numeric vector) If label is discrete (e.g. a clustering, developmental stage, treatment), one or more character values to match against. If label is continuous (e.g. pseudotime), should be a numeric vector or length 2 that describes the inclusive range of acceptable values.
label.type	(Character) Where to look for the data. Default is "search" which looks in order: "meta", "group", "sig", "gene", "counts", "pseudotime", "pca", "diff.data"

Value

(Character vector) Cell that match the criteria specified.

Examples

# Find cells from dome stage
whichCells(urd.object, "STAGE", "ZFDOME")

# Find cells with 500-1000 genes detected
whichCells(urd.object, "NUM_GENES", c(500,1000))

# Find cells with pseudotime between 0.54-0.72
whichCells(urd.object, "pseudotime", c(0.54,0.72))

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.