Adapt convertArray method for EPICv2 chip. Fix a bug in convertArray …

[AmericanoAndAlcohol]

…method.

[komalsrathi]

Hi @AmericanoAndAlcohol thanks for this. I am not the author but was looking for something like this. The only change I would suggest is adding the following after https://github.com/AmericanoAndAlcohol/minfi/blob/feature-fix/combine-arrays/R/combineArrays.R#L54.

probes2$Name <- gsub("_.*", "", probes2$Name)

This is because the EPIC v2 Name column is actually the Illumina ID so you need to remove the suffix after the underscore to match with the EPIC v1 Name column.

# EPIC v1 probes
> head(probes1)
DataFrame with 6 rows and 8 columns
         Name    AddressA    AddressB       Color       NextBase               ProbeSeqA               ProbeSeqB      nCpG
  <character> <character> <character> <character> <DNAStringSet>          <DNAStringSet>          <DNAStringSet> <integer>
1  cg18478105    46761277    86644198         Grn              C AAATAAATTT...ACAAAAACCA AAATAAATTT...ACGAAAACCG         5
2  cg09835024    16745152    81631976         Red              A AATAAACACC...ACAAAAATCA AATAAACGCC...ACAAAAATCG         5
3  cg14361672    51800947     7743487         Red              T ATCACTACCT...ACATCCTACA ATCACTACCT...ACATCCTACG         2
4  cg01763666    37768834    23754592         Grn              C AAACAAAAAT...AAAACAAACA GAACAAAAAT...AAAACAAACG         1
5  cg12950382     8726444    76660327         Red              A ATACCAAAAA...CCAAATAACA GTACCGAAAA...CCGAATAACG         3
6  cg02115394    68602543    59659581         Red              A AAAATCACTA...AAAAAACTCA AAAATCGCTA...AAAAAACTCG         4

# EPIC v2 probes
> head(probes2)
DataFrame with 6 rows and 8 columns
             Name    AddressA    AddressB       Color       NextBase               ProbeSeqA               ProbeSeqB      nCpG
      <character> <character> <character> <character> <DNAStringSet>          <DNAStringSet>          <DNAStringSet> <integer>
1 cg25324105_BC11     1754126    99753217         Red              A ATTTATAAAC...TTCACAACCA GTTTATAAAC...TTCGCGACCG         3
2 cg25383568_TC11    79792482    69667133         Grn              C AAACCAAAAA...TTAAAAAACA AAACCGAAAA...TTAAAAAACG         2
3 cg25455143_BC11    80699190     7659147         Red              T ATAAAAAAAA...CTCAAAATCA ATAAAAAAAA...CTCGAAATCG         2
4 cg25459778_BC11    60797262    65710482         Grn              C AAAAATTTAA...ATCAAAACCA AAAAATTTAA...GTCGAAACCG         5
5 cg25487775_BC11     5799427    89606481         Red              A AAAAACAACC...AAAAAACACA AAAAACAACC...AAAAAACGCG         1
6 cg25595446_BC11    65640459    39619855         Grn              C AATAAAAATA...AAAATAAACA AATAAAAATA...AAAATAAACG         4