A function to selectec top X on the basis of gene/transcript expression

This function select the X top genes given a user defined threshold

topx(
  group = c("sudo", "docker"),
  file,
  threshold,
  separator,
  logged = FALSE,
  type = c("expression", "variance")
)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs

file,

a character string indicating the path of the file. IMPORTANT: full path to the file MUST be included

threshold,

integer used for filtering indicate the number of top expressed/vaying genes to be selected

separator,

separator used in count file, e.g. '\t', ','

logged,

boolean TRUE or FALSE, if FALSE gene expression data are log10 transformed before being plotted.

type,

expression refers to the selection of the top expressed genes, variance to the the selection of the top variable genes

Value

a filtered tab delimited file and a histogram of the gene by gene total expression

Author

Raffaele Calogero, raffaele.calogero [at] unito [dot] it, UNITO

Examples

if (FALSE) {

 system("wget http://130.192.119.59/public/singlecells_counts.txt.gz")
 system("gzip -d singlecells_counts.txt.gz")
 topx(group="docker", file=paste(getwd(), "singlecells_counts.txt", sep="/"),
       threshold=10000, logged=FALSE, type="expression", separator="\t")
       
 topx(group="docker", file=paste(getwd(), "singlecells_counts.txt", sep="/"), 
       threshold=10000, logged=FALSE, type="variance", separator="\t")
}