The question aboud the fisher.test in `trinucleotideMatrix`

Hi, Thanks for the great package, I'm learning APOBEC enrichemnt, after studying line by line. I have some questions about the fisher.test here:

maftools/R/TrinucleotideMatrix.R

Line 268 in 80b22a4

    
           xf = fisher.test(matrix(c(x[2], sum(x[3], x[4]), x[1] - x[2], x[3]-x[4]), nrow = 2), alternative = 'g')

For some test, I use debug(trinucleotideMatrix) to step into function trinucleotideMatrix, after running in fisher.test, I checked the apobec.fisher.dat which is presented here:

Browse[2]> apobec.fisher.dat
      n_C>G_and_C>T tCw_to_G+tCw_to_T     C  tcw  wga
 [1,]           121                24  1481  161  164
 [2,]           997               601 10364 1694 1679
 [3,]           743               245  8373 1100 1038
 [4,]           149                67  1647  230  250
 [5,]            85                19   984  147  127
 [6,]           356                71  3941  451  526
 [7,]          1091               483 11777 1757 1692
 [8,]           306               172  3334  553  486
 [9,]          1869              1233 19255 3112 3265
[10,]           681               322  7163 1083 1133
[11,]           658               197  7326  929  924
[12,]           353               185  3786  568  612

fisher.test is implemented row-wise:

apply(
    X = apobec.fisher.dat,
    1, function(x) {
        xf <- fisher.test(matrix(c(
            x[2], sum(x[3], x[4]),
            x[1] - x[2], x[3] - x[4]
        ), nrow = 2), alternative = "g")
        data.table::data.table(
            fisher_pvalue = xf$p.value,
            or = xf$estimate, ci.up = xf$conf.int[1], ci.low = xf$conf.int[2]
        )
    }
)

the matrix used to implement fisher.test is like something:

c(
    `tCw_to_G+tCw_to_T`,
    C + tcw,  
    `n_C>G_and_C>T` - `tCw_to_G+tCw_to_T`,
    C - tcw
)

The second and fourth value is I'm concered; from the orginal article:
to an analogous ratio for all cytosines and guanines that reside inside and outside of the tCw/wGa motif within a sample fraction of the genome.

I think the matrix for fisher.test should be something (including both cytosines and guanines) like this:

c(
    `tCw_to_G+tCw_to_T`, tcw + wga,
    `n_C>G_and_C>T` - `tCw_to_G+tCw_to_T`, C + G - (tcw + wga)
)

Please correct me if I'm wrong

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