getMCI_inner {BioTIP} | R 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

[Package BioTIP version 1.4.0 Index]