I am trying to use regionCount from gRanges on methylKit datasets and I get fewer rows than expected.

For instance I have a the CpG entries from mm10 in one dataset (geneC.obj) and the methylation counts in another (methC) I only get 5 rows returned instead of what the equivalent of bedtools map -b methC -a geneC.obj which returns about 16010 entries (after turning these data sets into bed files)

>bedtools map -b methC.bed -a geneC.obj.cpg.bed -c 5 -o mean|wc -l
   16010

Can some explain to me what I am doing wrong or thinking wrong?

rcCpgC<-regionCounts(methC, geneC.obj$cpg,chunk.size=100)
> rcCpgC

methylBase object with 5 rows

--------------
    chr    start      end strand coverage1 numCs1 numTs1 coverage2 numCs2
1  chr8 19784573 19785241      +        73     11     62       151     27
2  chr8 20122210 20122868      +        72      9     63       130     33
3 chr11  3192998  3193699      +      1683   1466    217      2451   2079
4 chr17 39843169 39846346      +     55945  10077  45868     72620  12448
5 chr17 39848221 39848823      +      6816   1124   5692      9133   1192
  numTs2 coverage3 numCs3 numTs3 coverage4 numCs4 numTs4
1    125        64      9     55        88     33     55
2     97        77     21     56       113     46     67
3    369      1670   1426    244      1906   1617    289
4  60170     52092  10164  41928     65223  12554  52674
5   7942      5595    909   4686      7139   1268   5871
--------------
sample.ids: TsixUn1 TsixD TsixX TsixXD 
destranded TRUE 
assembly: mm10 
context: CpG 
treament: 0 1 2 3 
resolution: region 

-------------
methC
methylBase object with 2034 rows
--------------
   chr    start      end strand coverage1 numCs1 numTs1 coverage2 numCs2
1 chr1 59347355 59347355      +        29     28      1        25     22
2 chr1 59347426 59347426      +        40     38      2        42     37
3 chr1 59347454 59347454      +        41     34      7        42     36
4 chr1 59347460 59347460      +        41     38      3        39     36
5 chr1 59347474 59347474      +        37     33      4        38     35
6 chr1 66272056 66272056      +        21     19      2        25     19
  numTs2 coverage3 numCs3 numTs3 coverage4 numCs4 numTs4
1      2        27     26      1        24     23      1
2      5        40     39      1        29     25      4
3      6        39     33      6        24     15      9
4      3        36     36      0        24     22      2
5      3        33     29      4        19     18      1
6      6        15     14      1        18     18      0
--------------
sample.ids: TsixUn1 TsixD TsixX TsixXD 
destranded TRUE 
assembly: mm10 
context: CpG 
treament: 0 1 2 3 
resolution: base 
-------------------------------
geneC.obj$cpg
GRanges object with 16010 ranges and 2 metadata columns:
          seqnames            ranges strand |     score        name
             <Rle>         <IRanges>  <Rle> | <numeric> <character>
      [1]     chr1   3531625-3531843      + |         0           0
      [2]     chr1   3670620-3671074      + |         0           0
      [3]     chr1   3671655-3672156      + |         0           0
      [4]     chr1   4491702-4493673      + |         0           0
      [5]     chr1   4496948-4497608      + |         0           0
      ...      ...               ...    ... .       ...         ...
  [16006]     chrY 90793290-90793819      + |         0           0
  [16007]     chrY 90818330-90818565      + |         0           0
  [16008]     chrY 90824267-90824502      + |         0           0
  [16009]     chrY 90825141-90829322      + |         0           0
  [16010]     chrM              2-10      + |         0           0
  -------
  seqinfo: 22 sequences from an unspecified genome; no seqlengths
>

R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.4.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] plyranges_1.19.0      genomationData_1.32.0 genomation_1.32.0    
 [4] BRGenomics_1.12.0     rtracklayer_1.60.1    volcano3D_2.0.9      
 [7] methylKit_1.26.0      GenomicRanges_1.52.1  GenomeInfoDb_1.36.4  
[10] IRanges_2.34.1        S4Vectors_0.38.2      BiocGenerics_0.46.0  

loaded via a namespace (and not attached):
  [1] splines_4.3.3               BiocIO_1.10.0              
  [3] matrixTests_0.2.3           bitops_1.0-7               
  [5] ggplotify_0.1.2             tibble_3.2.1               
  [7] R.oo_1.26.0                 polyclip_1.10-6            
  [9] XML_3.99-0.16.1             lifecycle_1.0.4            
 [11] rstatix_0.7.2               edgeR_3.42.4               
 [13] doParallel_1.0.17           vroom_1.6.5                
 [15] lattice_0.22-6              MASS_7.3-60.0.1            
 [17] backports_1.4.1             magrittr_2.0.3             
 [19] plotly_4.10.4               limma_3.56.2               
 [21] plotrix_3.8-4               yaml_2.3.8                 
 [23] cowplot_1.1.3               DBI_1.2.2                  
 [25] RColorBrewer_1.1-3          ConsensusClusterPlus_1.64.0
 [27] pkgload_1.3.4               abind_1.4-5                
 [29] zlibbioc_1.46.0             purrr_1.0.2                
 [31] R.utils_2.12.3              ggraph_2.2.1               
 [33] RCurl_1.98-1.14             yulab.utils_0.1.4          
 [35] tweenr_2.0.3                circlize_0.4.16            
 [37] GenomeInfoDbData_1.2.10     enrichplot_1.20.3          
 [39] ggrepel_0.9.5               tidytree_0.4.6             
 [41] codetools_0.2-20            DelayedArray_0.26.7        
 [43] DOSE_3.26.2                 ggforce_0.4.2              
 [45] tidyselect_1.2.1            shape_1.4.6.1              
 [47] aplot_0.2.2                 farver_2.1.1               
 [49] viridis_0.6.5               matrixStats_1.2.0          
 [51] GenomicAlignments_1.36.0    jsonlite_1.8.8             
 [53] GetoptLong_1.0.5            tidygraph_1.3.1            
 [55] iterators_1.0.14            bbmle_1.0.25.1             
 [57] foreach_1.5.2               tools_4.3.3                
 [59] treeio_1.24.3               Rcpp_1.0.12                
 [61] glue_1.7.0                  mnormt_2.1.1               
 [63] gridExtra_2.3               mgcv_1.9-1                 
 [65] xfun_0.43                   DESeq2_1.40.2              
 [67] qvalue_2.32.0               MatrixGenerics_1.12.3      
 [69] dplyr_1.1.4                 withr_3.0.0                
 [71] numDeriv_2016.8-1.1         BiocManager_1.30.22        
 [73] fastmap_1.1.1               fansi_1.0.6                
 [75] digest_0.6.35               R6_2.5.1                   
 [77] gridGraphics_0.5-1          seqPattern_1.32.0          
 [79] colorspace_2.1-0            GO.db_3.17.0               
 [81] gtools_3.9.5                RSQLite_2.3.6              
 [83] R.methodsS3_1.8.2           utf8_1.2.4                 
 [85] tidyr_1.3.1                 generics_0.1.3             
 [87] data.table_1.15.4           htmlwidgets_1.6.4          
 [89] graphlayouts_1.1.1          httr_1.4.7                 
 [91] S4Arrays_1.0.6              scatterpie_0.2.1           
 [93] pkgconfig_2.0.3             gtable_0.3.4               
 [95] blob_1.2.4                  impute_1.74.1              
 [97] ComplexHeatmap_2.16.0       XVector_0.40.0             
 [99] htmltools_0.5.8             clusterProfiler_4.8.3      
[101] shadowtext_0.1.3            carData_3.0-5              
[103] fgsea_1.26.0                clue_0.3-65                
[105] scales_1.3.0                Biobase_2.60.0             
[107] logging_0.10-108            png_0.1-8                  
[109] ggfun_0.1.4                 ggdendro_0.2.0             
[111] knitr_1.45                  rstudioapi_0.16.0          
[113] tzdb_0.4.0                  reshape2_1.4.4             
[115] rjson_0.2.21                coda_0.19-4.1              
[117] nlme_3.1-164                bdsmatrix_1.3-7            
[119] cachem_1.0.8                GlobalOptions_0.1.2        
[121] stringr_1.5.1               KernSmooth_2.23-22         
[123] parallel_4.3.3              HDO.db_0.99.1              
[125] RcppZiggurat_0.1.6          AnnotationDbi_1.62.2       
[127] restfulr_0.0.15             pillar_1.9.0               
[129] reshape_0.8.9               vctrs_0.6.5                
[131] ggpubr_0.6.0                car_3.1-2                  
[133] cluster_2.1.6               DEGreport_1.36.0           
[135] readr_2.1.5                 mvtnorm_1.2-4              
[137] cli_3.6.2                   locfit_1.5-9.9             
[139] compiler_4.3.3              Rsamtools_2.16.0           
[141] rlang_1.1.3                 crayon_1.5.2               
[143] ggsignif_0.6.4              mclust_6.1                 
[145] emdbook_1.3.13              plyr_1.8.9                 
[147] fs_1.6.3                    stringi_1.8.3              
[149] psych_2.4.3                 gridBase_0.4-7             
[151] viridisLite_0.4.2           BiocParallel_1.34.2        
[153] munsell_0.5.1               Biostrings_2.68.1          
[155] lazyeval_0.2.2              GOSemSim_2.26.1            
[157] Matrix_1.6-5                BSgenome_1.68.0            
[159] hms_1.1.3                   patchwork_1.2.0            
[161] bit64_4.0.5                 ggplot2_3.5.0              
[163] KEGGREST_1.40.1             SummarizedExperiment_1.30.2
[165] fastseg_1.46.0              Rfast_2.1.0                
[167] igraph_2.0.3                broom_1.0.5                
[169] memoise_2.0.1               RcppParallel_5.1.7         
[171] ggtree_3.8.2                fastmatch_1.1-4            
[173] bit_4.0.5                   downloader_0.4             
[175] ape_5.7-1                   gson_0.1.0