Example output from
dmrseq function run on the
a data.frame that contains the results of the inference. The data.frame contains one row for each candidate region, and 10 columns, in the following order: 1. chr = chromosome, 2. start = start basepair position of the region, 3. end = end basepair position of the region, 4. indexStart = the index of the region's first CpG, 5. indexEnd = the index of the region's last CpG, 6. L = the number of CpGs contained in the region, 7. area = the sum of the smoothed beta values 8. beta = the coefficient value for the condition difference, 9. stat = the test statistic for the condition difference, 10. pval = the permutation p-value for the significance of the test statistic, and 11. qval = the q-value for the test statistic (adjustment for multiple comparisons to control false discovery rate).
Obtained from running the examples in
A script which executes these steps
and constructs the
object may be found in ‘inst/scripts/get_dmrs.ex.R’
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