corrDNA (version 1.0.1)

assoc_comb: Complete association matrix.

Description

All the six possible association matrices can be merged in to a single matrix to visualize the overall association among positions as well as among the occurences of nucleotides of different positions, in a position-wise aligned sequence dataset.

Usage

assoc_comb(x, rZiZj, rZiZjR, rZiZjY, rZiRZjR, rZiRZjY, rZiYZjY)

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.

rZiRZjR

An object generated by using the function assoc_ZiR.ZjR.

rZiRZjY

An object generated by using the function assoc_ZiR.ZjY.

rZiYZjY

An object generated by using the function assoc_ZiY.ZjY.

Value

A numeric matrix of order 3L by 3L for the dataset of L nucleotides long sequences.

Details

All the six association matrices are required to be generated prior to merging them into a single matrix.

Examples

# NOT RUN {
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)
zirzjr <- assoc_ZiR.ZjR(x=kk,rZiZj=zizj,rZiZjR=zizjr)
zirzjy <- assoc_ZiR.ZjY(x=kk,rZiZj=zizj,rZiZjR=zizjr,rZiZjY=zizjy)
ziyzjy <- assoc_ZiY.ZjY(x=kk,rZiZj=zizj,rZiZjY=zizjy)
fin_corr <- assoc_comb(x=kk, rZiZj=zizj,rZiZjR=zizjr,rZiZjY=zizjy,
rZiRZjR=zirzjr,rZiRZjY=zirzjy,rZiYZjY=ziyzjy)
fin_corr
# }