topx: A function to selectec top X on the basis of gene/transcript...

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

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

Description

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

Usage

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(s)

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

Examples

## Not run: 

 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")

## End(Not run)

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