This dataset has been analyzed and provided by the listed reference. There
are around 22,000 cytosines, each of which is under two conditions. For each
cytosine under each condition, there is only one replicate. The discrete
count for each replicate can be modeled by binomial distribution, and
Fisher's exact test can be applied to assess if a cytosine is differentially
methylated. The filtered data lister contains cytosines whose
total counts for both lines are greater than 5 and whose count for each line
does not exceed 25.
data("listerdata")data("listerdata_four_columns")
listerdata is a data.frame with 3,525 rows and the following two
columns:
Degree of methylation of the i-th cytosine in reference genome.
Degree of methylation of the i-th cytosine in mutated genome.
Thus, each row describes a 2x2 table:
| AT1G01070.1 | This cytosine | All other cytosines |
| Col0 counts | \(X_{i, 1}\) | 34,244 - \(X_{i, 1}\) |
| Met13 counts | \(X_{i, 2}\) | 39,342 - \(X_{i, 2}\) |
listerdata_four_columns is a data.frame with 3,525 rows and the
following four columns:
Degree of methylation of the i-th cytosine in reference genome.
Degree of methylation of the i-th cytosine in mutated genome.
Degree of methylation of all other cytosines in reference genome.
Degree of methylation of all other cytosines in mutated genome.
| AT1G01070.1 | This cytosine | All other cytosines |
| Col0 counts | \(X_{i, 1}\) | \(X_{i, 3}\) |
| Met13 counts | \(X_{i, 2}\) | \(X_{i, 4}\) |
Lister, R., O'Malley, R., Tonti-Filippini, J., Gregory, B. D., Berry, C. C., Millar, A. H. & Ecker, J. R. (2008). Highly integrated single-base resolution maps of the epigenome in arabidopsis, Cell 133(3), pp. 523-536. tools:::Rd_expr_doi("https://doi.org/10.1016/j.cell.2008.03.029")