listerdata: Lister data

In DiscreteDatasets: Example Data Sets for Use with Discrete Statistical Tests

Lister data

Description

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.

Usage

data("listerdata")

data("listerdata_four_columns")

Format

listerdata is a data.frame with 3,525 rows and the following two columns:

Col0_Counts

Degree of methylation of the i-th cytosine in reference genome.

Met13_Counts

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:

Col0_Counts.ThisCyto

Degree of methylation of the i-th cytosine in reference genome.

Met13_Counts.ThisCyto

Degree of methylation of the i-th cytosine in mutated genome.

Col0_Counts.AllOtherCytos

Degree of methylation of all other cytosines in reference genome.

Met13_Counts.AllOtherCytos

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}

Note

The original listerdata dataset has been taken from the fdrDiscreteNull package.

References

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. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1016/j.cell.2008.03.029")}

DiscreteDatasets documentation built on April 4, 2025, 2:22 a.m.