getMCI_inner {BioTIP} | R Documentation |
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.
getMCI_inner( members, countsL, adjust.size, fun = c("cor", "BioTIP"), PCC_gene.target = "zero", M = NULL )
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'. |
A vector recording one MCI score per state.
Zhezhen Wang zhezhen@uchicago.edu; Xinan H Yang xyang2@uchicago.edu