Hello I am using MethylKIT package for WGBS Data analysis. There I have observed that whatever input I am giving, in the meth object, actually a certain percent of input data is going for downstream analysis.

                      Chr   base    strand  coverage    freqT   freqC

53297621 chr21 6555133 + 13 38.4615384615385 61.5384615384615 53297622 chr21 6555134 - 25 48 52 53297623 chr21 6555143 + 14 7.14285714285714 92.8571428571429 53297624 chr21 6555144 - 30 30 70 53297625 chr21 6555145 + 14 7.14285714285714 92.8571428571429 53297626 chr21 6555146 - 29 3.44827586206897 96.551724137931

My input data was like that of dimension 857673, but when I made the meth object, the dimension of that is only a certain percent. Why is that so?