houseKeep: houseKeep Filtering

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

houseKeep Filtering

Description

This function filter your matrix count on a specific gene house keepin list

Usage

houseKeep(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  separator,
  logTen,
  geneNameControl = 1,
  houseK,
  topCell
)

Arguments

group,	a character string. Two options: sudo or docker, depending to which group the user belongs
scratch.folder,	a character string indicating the path of the scratch folder
file,	a character string indicating the path of the file, with file name and extension included
separator,	separator used in count file, e.g. '\t', ','
logTen,	0 if is raw count, 1 otherwise
geneNameControl,	0 if the matrix has gene name without ENSEMBL geneID. 1 if the gene names is formatted as: ENSMUSG00000000001:Gnai3. If the gene names is made only by ensamble name, scannoByGtf has to be run first.
houseK,	to be described ....
topCell,	to be described ...

Value

return matrix filtered by the best cells that have housekeepin genes most expressed

Author(s)

Luca Alessandri , alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

## Not run: 
housekeep("docker","/home/lucastormreig/scratch/","/home/lucastormreig/CASC7.2/6_1hfc/Data/random_10000_filtered_annotated_lorenz_naive_penta2_0",6,",","naive")#

## End(Not run)

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