filterset {FateID}

Function for filtering expression data

Description

This function discards lowly expressed genes from the expression data frame.

Usage

filterset(x, n = NULL, minexpr = 2, minnumber = 1)

Arguments

x

expression data frame with genes as rows and cells as columns. Gene IDs should be given as row names and cell IDs should be given as column names.

n

ordered vector of cell IDs to be included. Cell IDs need to be column names of x. If not provided, then all cell IDs are included in arbitray order. Default value is NULL.

minexpr

positive real number. This is the minimum expression required for at least minnumber cells. All genes that do not fulfill this criterion are removed. The default value is 2.

minnumber

positive integer number. This is the minimum number of cells in which a gene needs to be expressed at least at a level of minexpr. All genes that do not fulfill this criterion are removed. The default value is 1.

Value

Reduced expression data frame with genes as rows and cells as columns in the same order as in n.