assoc_ZiR.ZjY {corrDNA}

Association between variable Z_{iR} and Z_{jY}.

Description

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

Usage

assoc_ZiR.ZjY(x, rZiZj, rZiZjR, rZiZjY)

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.

rZiZjR

An object generated by using the function assoc_Zi.ZjR.

rZiZjY

An object generated by using the function assoc_Zi.ZjY.

Details

The user has to supply the input dataset as well as the outputs generated from the functions assoc_Zi.Zj, assoc_Zi.ZjR and assoc_Zi.ZjY.

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)
zizjy <- assoc_Zi.ZjY(x=kk, rZiZj=zizj)
zirzjy <- assoc_ZiR.ZjY(x=kk, rZiZj=zizj, rZiZjR=zizjr, rZiZjY=zizjy)
zirzjy