Running cpgCollapse on a GenomicRatioSet is seemingly removing all the feature names. 

> featureNames(gset)
   [1] "cg13869341"  "cg14008030"  "cg12045430"  "cg20826792"  "cg00381604" 
   [6] "cg20253340"  "cg21870274"  "cg03130891"  "cg24335620"  "cg16162899" 
  [11] "cg17149495"  "cg22802167"  "cg24669183"  "cg17308840"  "cg17866181" 
  [16] "cg24159721"  "cg15174812"  "cg08477687"  "cg00034556"  "cg00645010"

Running cpgCollapse:

> collapsingGset <- cpgCollapse(gset, what = c("Beta", "M"), maxGap = 500,

            blockMaxGap = 2.5 * 10^5, maxClusterWidth = 1500,

            dataSummary = colMeans, na.rm = FALSE,

            returnBlockInfo = TRUE, islandAnno = NULL, verbose = TRUE)

> collapsedGset <- collapsingGset[[1]]

> featureNames(collapsedGset)
NULL

Which results in numerical rownames with nondescriptive information.​

> betas <- as.data.frame(getBeta(collapsedGset))
> rownames(betas)
   [1] "1"    "2"    "3"    "4"    "5"    "6"    "7"    "8"    "9"    "10"   "11" 
  [12] "12"   "13"   "14"   "15"   "16"   "17"   "18"   "19"   "20"   "21"   "22"  

Is there a way to view the new feature names that have been assigned to the GenomicRatioSet after running cpgCollapse? Otherwise, I haven't any idea what the beta values correspond to. 

The featureNames you had previously aren't informative! Unless something like cg14008030 has some inherent meaning that I cannot infer.

Anyway, the returned GenomicRatioSet contains a GRanges object that tells you the genomic location of whatever it is that you have in that GenomicRatioSet, which is in fact informative. An example:

> library(minfi)
> library(minfiData)
> gmSet <- preprocessQuantile(MsetEx)
[preprocessQuantile] Mapping to genome.
[preprocessQuantile] Fixing outliers.
[preprocessQuantile] Quantile normalizing.

> granges(gmSet)
GRanges object with 485512 ranges and 0 metadata columns:
             seqnames               ranges strand
                <Rle>            <IRanges>  <Rle>
  cg13869341     chr1       [15865, 15865]      *
  cg14008030     chr1       [18827, 18827]      *
  cg12045430     chr1       [29407, 29407]      *
  cg20826792     chr1       [29425, 29425]      *
  cg00381604     chr1       [29435, 29435]      *
         ...      ...                  ...    ...
  cg17939569     chrY [27009430, 27009430]      *
  cg13365400     chrY [27210334, 27210334]      *
  cg21106100     chrY [28555536, 28555536]      *
  cg08265308     chrY [28555550, 28555550]      *
  cg14273923     chrY [28555912, 28555912]      *
  -------
  seqinfo: 24 sequences from hg19 genome; no seqlengths

So for each probe, we have the genomic location. Now let's collapse

>  z <- cpgCollapse(gmSet)
> granges(z[[1]])
GRanges object with 223497 ranges and 3 metadata columns:
           seqnames               ranges strand |        id        type
              <Rle>            <IRanges>  <Rle> | <numeric> <character>
       [1]     chr1       [15865, 15865]      * |         1     OpenSea
       [2]     chr1       [18827, 18827]      * |         2     OpenSea
       [3]     chr1       [29407, 29435]      * |         3      Island
       [4]     chr1       [68849, 68849]      * |         4     OpenSea
       [5]     chr1       [69591, 69591]      * |         5     OpenSea
       ...      ...                  ...    ... .       ...         ...
  [223493]     chrY [25314171, 25314171]      * |    223493     OpenSea
  [223494]     chrY [26716289, 26716289]      * |    223494     OpenSea

           blockgroup
            <numeric>
       [1]          1
       [2]          1
       [3]       <NA>
       [4]          1
       [5]          1
       ...        ...
  [223493]       1049
  [223494]       1050
  [223495]       1051
 
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths

And we can look to see how many CpGs go into these blocks

> table(table(width(granges(z[[1]]))))

     1      2      3      4      5      6      7      8      9     10     11
   609    143     49     44     37     49     47     44     53     43     47
    12     13     14     15     16     17     18     19     20     21     22
    47     39     52     43     38     33     47     42     35     42     34
    23     24     25     26     27     28     29     30     31     32     33
    32     20     27     35     29     27     36     29     21     22     26
    34     35     36     37     38     39     40     41     42     43     44
    10     20     18     20     17     19     13      9      9     10     13
    45     46     47     48     49     50     51     52     53     54     55
    11     13     10     11     14      4      8      6     10     14     11
    56     57     58     59     60     61     62     63     64     65     66
     9      5     11      3     11     10     13     15     10     11      7
    67     68     69     70     71     72     73     74     75     76     77
    12      7      6      9     10      4      9      6      7     11      7
    78     79     80     81     82     83     84     85     86     87     88
     5      8     17      4      8      9      9      7      3      8      3
    89     90     91     92     93     94     95     96     97     98     99
     6     11      3      4      9      8     11      4      5      6      8
   100    101    102    103    104    105    106    107    108    109    110
     5     12      5      8      9      7     10      8      9     11     10
   111    112    113    114    115    116    117    118    119    120    121
     5     11      4      8      7      7      2     10      6      3      2
   122    123    124    126    127    128    129    130    133    134    146
     3      6      2      2      2      2      1      2      1      1      2
145014
     1
>