R/FindComethylatedRegions.R
FindComethylatedRegions.RdFind contiguous comethylated regions based on output file from
function MarkComethylatedCpGs
FindComethylatedRegions(CpGs_df, minCpGs_int = 3)an output dataframe from function MarkComethylatedCpGs,
with variables: CpG, keep, ind, r_drop. See details in documentation
for MarkComethylatedCpGs.
an integer indicating the minimum number of CpGs for output genomic regions
A data frame with variables ProbeID and Subregion (index for each output contiguous comethylated region)
data(betaMatrix_ex4)
CpGs_df <- MarkComethylatedCpGs(betaCluster_mat = betaMatrix_ex4)
FindComethylatedRegions(CpGs_df)
#> ProbeID Subregion
#> 1 cg05076221 1
#> 2 cg23936031 1
#> 3 cg02248486 1
#> 4 cg25866143 1
#> 5 cg09549073 1
#> 6 cg01370449 1
#> 7 cg04863892 1
#> 8 cg19759481 1
#> 9 cg12128839 1
#> 10 cg02916332 1
#> 11 cg17569124 1
#> 12 cg02005600 1
#> 13 cg25307665 1
#> 14 cg14014955 1
#> 15 cg02646423 1
#> 17 cg23204968 2
#> 18 cg05835726 2
#> 19 cg14058329 2
#> 20 cg03207666 2
#> 21 cg13512268 2
#> 22 cg23454797 2
#> 23 cg12015737 2
#> 24 cg08070327 2
#> 25 cg25506432 2
#> 26 cg14658493 2
#> 27 cg19196335 2
#> 28 cg09880291 2
#> 29 cg24389585 2
#> 30 cg16997642 2
#> 31 cg20817131 2
#> 32 cg14013695 2
#> 33 cg25390165 2
#> 34 cg01323381 2
#> 36 cg05774699 3
#> 37 cg26023912 3
#> 38 cg14882265 3
#> 39 cg17432857 3
#> 40 cg00969405 3
#> 41 cg07049592 3
#> 42 cg02106682 3
#> 43 cg03368099 3
#> 44 cg01748892 3
#> 45 cg13694927 3
#> 46 cg03744763 3
#> 47 cg27151303 3
#> 48 cg05579037 3
#> 49 cg21641458 3
#> 50 cg09343092 3
#> 51 cg18931036 3
#> 52 cg24040595 3