Description Usage Arguments Details Value Author(s) Examples
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.
1 | assoc_comb(x, rZiZj, rZiZjR, rZiZjY, rZiRZjR, rZiRZjY, rZiYZjY)
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x |
A dataframe of position wise aligned sequence dataset having A, T, G and C only. |
rZiZj |
An object generated by using the function |
rZiZjR |
An object generated by using the function |
rZiZjY |
An object generated by using the function |
rZiRZjR |
An object generated by using the function |
rZiRZjY |
An object generated by using the function |
rZiYZjY |
An object generated by using the function |
All the six association matrices are required to be generated prior to merging them into a single matrix.
A numeric matrix of order 3L by 3L for the dataset of L nucleotides long sequences.
Prabina Kumar Meher & A. R. Rao
1 2 3 4 5 6 7 8 9 10 11 | 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
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