Accessor for the methylation (beta value) matrix

Retrieves the sites × samples matrix of methylation beta values from a commaData object. Values are in the range 0–1 (proportion of reads called methylated). Sites below the min_coverage threshold set at object creation are NA.

Usage

methylation(object)

# S4 method for class 'commaData'
methylation(object)

Arguments

object

A commaData object.

Value

A numeric matrix with rows corresponding to methylation sites and columns corresponding to samples. Rownames are site keys ("chrom:position:strand:mod_type"); column names are sample names.

See also

coverage, siteInfo, sampleInfo

Examples

data(comma_example_data)
m <- methylation(comma_example_data)
dim(m)
#> [1] 300   6
head(m)
#>                       ctrl_1    ctrl_2    ctrl_3    treat_1   treat_2   treat_3
#> chr_sim:444:+:6mA  0.9048367 0.8237897 0.8517928 0.30677235 0.4768195 0.4124745
#> chr_sim:1072:+:6mA 0.8128778 0.8501235 0.9732947 0.74361241 0.8354918 0.9364048
#> chr_sim:1600:-:6mA 0.8581977 0.8124665 0.9528697 0.94747731 0.9132681 0.9212486
#> chr_sim:2176:+:6mA 0.9033107 0.8708096 0.9598866 0.02648254 0.5052399 0.2795380
#> chr_sim:3565:+:6mA 0.8558892 0.9512447 0.9277963 0.88531486 0.9560292 0.9166728
#> chr_sim:4767:-:6mA 0.7848818 0.8599388 0.9546899 0.91202669 0.9682563 0.9142556