Differential methylation test using a beta-binomial approach
The function calculates differential methylation statistics between two groups of samples. This is the main function of the methylSig package, and the method most users should use to test for differentially methylated CpGs (DMCs) or differentially methylated regions (DMRs). The function uses a Beta-binomial approach to calculate differential methylation statistics, accounting for variation among samples within each group.
Arguments
bs a BSseq object possibly having passed through prior filtering and tiling functions.
group a character string indicating the column of colData(bs) to use to determine group membership.
case a character string indicating the factor in group that is considered the case. Loci with positive methylation changes correspond to hyper-methylation in this factor (and hypo-methylation in control).
control a character string indicating the factor in group that is considered the control. Loci with negative methylation changes correspond to hyper-methylation in this factor (and hypo-methylation in case).
Values
A GRanges object corresponding to loci tested and mcols with the test results. In particular,
phi_common_est
log_lik_ratio
df
case_meth
control_meth
meth_diff
direction
pvalue
fdr
Tests
On small test data with clear methylation differences, test for correct calls.
Function call
diff_methylsig(bs, group, case, control)Description
Differential methylation test using a beta-binomial approach
The function calculates differential methylation statistics between two groups of samples. This is the main function of the methylSig package, and the method most users should use to test for differentially methylated CpGs (DMCs) or differentially methylated regions (DMRs). The function uses a Beta-binomial approach to calculate differential methylation statistics, accounting for variation among samples within each group.
Arguments
bsaBSseqobject possibly having passed through prior filtering and tiling functions.groupacharacterstring indicating the column ofcolData(bs)to use to determine group membership.caseacharacterstring indicating the factor ingroupthat is considered the case. Loci with positive methylation changes correspond to hyper-methylation in this factor (and hypo-methylation incontrol).controlacharacterstring indicating the factor ingroupthat is considered the control. Loci with negative methylation changes correspond to hyper-methylation in this factor (and hypo-methylation incase).Values
A
GRangesobject corresponding to loci tested andmcolswith the test results. In particular,Tests
On small test data with clear methylation differences, test for correct calls.