R.SCORE: R.SCORE

In wycwycpku/RSCORE: RSCORE (R-package of Single-Cell mOleculaR nEtwork)

Description

explore single-cell RNA-seq data with the view of molecular networks.

Usage

R.SCORE(
  Data,
  PPI = "Biogrid",
  species = 9606,
  score_threshold = 600,
  metric = c("cor", "rho", "phi", "phs"),
  module_min = 3,
  max_step = 10,
  AUCRank = 400,
  SeqMethod = "10X",
  nCores = 1
)

Arguments

Data	gene*cell matrix or a seurat object.
PPI	protein-protein network, you can provide a matrix if you have PPI data, or you can let PPI = 'Biogrid' or 'String', the system will download corresponding PPI data.
species	NCBI taxonomy identifier of the species to query for homologs, default is 9606(Homosapiens), only needed when PPI = 'Biogrid' or 'String'.
score_threshold	threshold on the score of the interaction, default is 600, only needed when PPI = 'String'
metric	A character string. The metric used to calculate association. Choose one of 'cor', 'rho', 'phi', 'phs'
module_min	Integer number. The minimum size of a module to be accepted.
max_step	Integer number. The maximum step run in the community detect.
AUCRank	Integer number. The number of highly-expressed genes to include when computing AUCell.
SeqMethod	A charater string. Sequening methods, default is '10X'
nCores	Number of cores to use for computation.

Value

a seurat object

wycwycpku/RSCORE documentation built on Sept. 5, 2021, 4:25 p.m.