extract.cells: extract.cells

In iaconogi/bigSCale2: A framework for the analysis of single cell data (RNA-seq and ATAC-seq) including clustering,phenotyping,pseudotime and inferring gene regulatory networks.

Description

Works with the .mex files. It subsets to the specified set of cells and write them into the output .mex file.

Usage

extract.cells(input.mex, output.mex, cells, chuncks = 50000)

Arguments

input.mex	File name of the output dataset
cells	Indices of the cells you want to extract
chunks	A techincal parameter, you should not really touch this. It represent how large is the chunk of cells read when sequentially pharsing the input.mex

Value

Writes to disk the subsetted dataset. Please note that if cells will be automatially sorted. For example, is cells=c(10,1), meaning that you want to extract cells 10 and 1, the oupput matrix will contain, in order, cells 1 and 10.

Examples

check the online tutorial at Github

iaconogi/bigSCale2 documentation built on July 18, 2020, 8:21 p.m.