spatialAnalysis: spatial Analysis

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

spatial Analysis

Description

This function analyze the data that came up from permutationClustering script with spatial transcriptomics data.

Usage

spatialAnalysis(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nCluster,
  separator,
  tissuePosition
)

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
nCluster	Last number of cluster that has to be analyzed
separator	separator used in count file, e.g. '\t', ','
tissuePosition	file with tissue position name with extension

Value

stability plot for each nCluster,two files with score information for each cell for each permutation.

Author(s)

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

Examples

## Not run: 
spatialAnalysis(group="sudo", scratch.folder="/scratch", file="/home/lucastormreig/newDockers/data/matrix.csv",nCluster=13,separator=",",tissuePosition="/home/lucastormreig/newDockers/data/tissue_positions_list.csv")

## End(Not run)

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