filterZeros | R Documentation |
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)
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', ',' |
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.
Raffaele Calogero, raffaele.calogero [at] unito [dot] it, University of Torino
## 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)
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