getMCI_inner: Calculating MCI Score for randomly selected

View source: R/BioTIP_update_04202022.R

getMCI_innerR Documentation

Calculating MCI Score for randomly selected

Description

This function calculates random MCI score, allowing an estimation of correlation matrix using the Schafer-Strimmer Method for the PCC_in component in the MCI score.

Usage

getMCI_inner(
  members,
  countsL,
  adjust.size,
  fun = c("cor", "BioTIP"),
  PCC_gene.target = "zero",
  M = NULL
)

Arguments

members

An integer that is the length of genes in the CTS (critical transition signal).

countsL

A list of subset of dat matrix. The list length is the number of states. Each subset of matrix gives the genes in rows and samples in column.

adjust.size

A boolean value indicating if MCI score should be adjust by module size (the number of transcripts in the module) or not. Default FALSE.

fun

A character chosen between ("cor", "BioTIP"), indicating where an adjusted correlation matrix will be used to calculated the MCI score.

PCC_gene.target

A character 'zero' indicating that gene-gene correlation matrix will be shrunk. towards zero, used only for fun='BioTIP'.

M

is the overall shrunk correlation matrix, used only for fun='BioTIP'.

Value

A vector recording one MCI score per state.

Author(s)

Zhezhen Wang zhezhen@uchicago.edu; Xinan H Yang xyang2@uchicago.edu


xyang2uchicago/NPS documentation built on June 30, 2024, 10:15 p.m.