getMCI_inner: Calculating MCI Score for randomly selected

In xyang2uchicago/NPS: BioTIP: An R package for characterization of Biological Tipping-Point

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 [e-mail]; Xinan H Yang [e-mail]

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