assoc_Zi.ZjR {corrDNA}

Association between variable Z_{i} and Z_{jR}.

Description

Finding association between variable Z at i^{th} position and Z_{R} at j^{th} position. Here, the standard normal variable Z represents the occurence of R=(A,G) and Y=(C, T) at each position in the position wise aligned dataset, whereas the the standard normal variable Z_{R} reprsents the occurences of nucleotides A and G at any position based on some threshold value.

Usage

assoc_Zi.ZjR(x, rZiZj)

Arguments

x

A dataframe of position wise aligned sequence dataset having A, T, G and C only.

rZiZj

An object generated by using the function assoc_Zi.Zj.

Details

The user has to supply the input dataset as well as the output generated from the function assoc_Zi.Zj.

Value

A numeric matrix of order L by L for the dataset of L nucleotides long sequences.

Note

It may happen that the convergence will not reach after a ceratin number of iterations and will not produce any output. In such situation, the user is advised to exclude or include some positions , or otherwise include or exclude certain sequences. The user should exploit both options till convergence is reached.

Author(s)

Prabina Kumar Meher & A. R. Rao

Examples

data(don_dat)
kk <- don_dat[1:300,]
zizj <- assoc_Zi.Zj(x=kk)
zizjr <- assoc_Zi.ZjR(x=kk, rZiZj=zizj)
zizjr