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

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

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

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

Examples

if (FALSE) {
    #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")
}