filterZeros: A function plotting the distribution of zeros in cells...

In kendomaniac/CASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

A function plotting the distribution of zeros in cells eliminating all genes without a certain fraction of 0 in the samples

Description

This function plots the zeros distributions in cells and removes genes without a certain fraction of 0 in the samples

Usage

filterZeros(file, threshold = 0, sep)

Arguments

file,	a character string indicating the path of the cells un-normalized expression counts table
threshold,	a number from 0 to 1 indicating the fraction of max accepted zeros in each gene. 0 is set as default and it eliminates only genes having 0 in all cells.
sep,	separator used in count file, e.g. '\t', ','

Value

a PDF providing zeros distributions before removal of all genes without a certain fraction of 0 in the samples. A file with the prefix *filtered* in which the filtered data are saved.

Author(s)

Raffaele Calogero, raffaele.calogero [at] unito [dot] it, University of Torino

Examples

## Not run: 
    #downloading fastq files
    system("wget http://130.192.119.59/public/singlecells_counts.txt.gz")
    system("gzip -d singlecells_counts.txt.gz")
    filterZeros(file=paste(getwd(),"singlecells_counts.txt",sep="/"), threshold=0.1, sep="\t")

## End(Not run)

kendomaniac/CASC documentation built on Oct. 4, 2023, 11:10 a.m.