BCscWrapper: BCscTool_wrapper

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

BCscTool_wrapper

Description

The present function associates the clusters of two different and indipendent experiments using the Bray Curtis dissimilarity. Starting from the two original sets it takes only the genes common to both and calculates the Bray Curtis Dissimilarity between the clusters of one set and those of the other. all the results will be saved in the folder called "BCsc" inside the folder where the files of the first set are located

Usage

BCscWrapper(
  group = c("sudo", "docker"),
  setX,
  nclustX,
  markerX,
  setY,
  nclustY,
  markerY,
  separator = ",",
  scratch.folder,
  output.folder,
  pvalueComet = 1,
  subdivision = 10,
  starting_genes = 500,
  contamination = 5,
  permutation = 50,
  threshold = 3
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
setX	path to the first dataset
nclustX	number of cluster of the first dataset.
markerX	path to the FOLDER containing cluster-specific genes for the FIRST dataset. (after using Comet directory '.../nclustX/outputdata')
setY	path to the second dataset
nclustY	number of cluster of the second dataset
markerY	path to the FOLDER containing cluster-specific genes for the SECOND dataset. (after using Comet directory '.../nclustY/outputdata')
separator	separator used in both count file, e.g. '\t', ','
scratch.folder	a character string indicating the path of the scratch folder
output.folder	a character string indicating the path of the output folder to save analysis
pvalueComet	parameter to select only marker genes with a pvalue under a threshold value. DEFAULT = 1
subdivision	number of progressive reductions of the starting genes list. DEFAULT = 10
starting_genes	number of starting genes for each cluster selected from the main marker gene lists. DEFAULT = 500
contamination	percentage of genes to be contaminated at each permutation during the Bray-Curtis calculation. DEFAULT = 5
permutation	number of Bray-Curtis permutations. DEFAULT = 50
threshold	minimum value to consider a gene expressed in both count sets. DEFAULT VALUE: 3

Author(s)

Gabriele Piacenti, g [dot] pia91 [at] gmail [dot] com, University of Torino

Examples

		
## Not run: 
BCscWrapper(group="docker",
      setX = '/2tb/torino/piacenti/NT1_NT2/CRC0327_NT_1_clx/VandE/VandE.csv',
      nclustX = 7,
      markerX = '/2tb/torino/piacenti/NT1_NT2/CRC0327_NT_1_clx/VandE/Results/VandE/7/outputdata',
      setY = '/2tb/torino/piacenti/NT1_NT2/CRC0327_NT_2_clx/VandE/VandE.csv',
      nclustY = 8,
     markerY = '/2tb/torino/piacenti/NT1_NT2/CRC0327_NT_2_clx/VandE/Results/VandE/8/outputdata',
     scratch.folder = '/2tb/torino/piacenti/user09/piacenti/Prova_Prove/Script/scratch',
     output.folder = '/2tb/torino/piacenti/user09/piacenti/Prova_Prove/Script',
     pvalueComet = 1,
     subdivision = 10,
     starting_genes = 500,
     contamination = 5,
     permutation = 50,
     threshold = 3)

## End(Not run)

kendomaniac/rCASC documentation built on July 3, 2024, 6:05 a.m.