Question: Common probes between 27K and 450 chip
0
gravatar for Adrian Johnson
3.4 years ago by
Adrian Johnson330 wrote:

Hello:

I am interested in obtaining common probes between 27K and 450 chip.
Is there a way I could get the intersection of these two probes.

thanks

Adrian

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Adrian Johnson330
Answer: Common probes between 27K and 450 chip
0
gravatar for James W. MacDonald
3.4 years ago by
United States
James W. MacDonald52k wrote:

You can use the FDb.InfiniumMethylation.hg19 package for this purpose.

> library(FDb.InfiniumMethylation.hg19)

> z <- get450k()
Fetching coordinates for hg19...
> zz <- get27k()
Fetching coordinates for hg19...
> olap <- findOverlaps(z, zz)

> prb.450.in.27 <- z[queryHits(olap),]
> prb.27.in.450 <- zz[subjectHits(olap),]
> head(prb.450.in.27)
GRanges object with 6 ranges and 10 metadata columns:
             seqnames           ranges strand |    addressA    addressB channel
                <Rle>        <IRanges>  <Rle> | <character> <character>   <Rle>
  cg11876012    chr16 [101686, 101687]      * |    47645328                Both
  cg14820573    chr16 [102121, 102122]      * |    36735483                Both
  cg14747225    chr16 [103024, 103025]      * |    49673469                Both
  cg11653271    chr16 [103723, 103724]      * |    70653493                Both
  cg16003913    chr16 [127072, 127073]      * |    40707415                Both
  cg24399405    chr16 [189577, 189578]      * |    25772435                Both
             platform percentGC               sourceSeq probeType  probeStart
                <Rle> <numeric>          <DNAStringSet>     <Rle> <character>
  cg11876012     BOTH      0.36 TTTGTTACCT...CTGAATAGCG        cg      101638
  cg14820573     BOTH      0.44 CGTCAGTCTT...TGTTGTGGGA        cg      102073
  cg14747225     BOTH      0.54 AACAGCAAGT...TGAGAGATCG        cg      102976
  cg11653271     BOTH      0.64 CGCTCCCGGC...GGTCACTGCA        cg      103723
  cg16003913     BOTH      0.62 AAAAGGCCTT...GTGGGAGACG        cg      127072
  cg24399405     BOTH      0.44 GTTTAATTTA...CACTGCCTCG        cg      189577
                probeEnd probeTarget
             <character>   <numeric>
  cg11876012      101687      101686
  cg14820573      102122      102121
  cg14747225      103025      103024
  cg11653271      103772      103723
  cg16003913      127121      127072
  cg24399405      189626      189577
  -------
  seqinfo: 24 sequences from hg19 genome
> head(prb.27.in.450)
GRanges object with 6 ranges and 10 metadata columns:
             seqnames           ranges strand |    addressA    addressB channel
                <Rle>        <IRanges>  <Rle> | <character> <character>   <Rle>
  cg11876012    chr16 [101686, 101687]      * |     1740168      840379     Grn
  cg14820573    chr16 [102121, 102122]      * |     5550563      510215     Red
  cg14747225    chr16 [103024, 103025]      * |     6940102     7200070     Red
  cg11653271    chr16 [103723, 103724]      * |     6270176     3290487     Grn
  cg16003913    chr16 [127072, 127073]      * |     3400600     1340327     Grn
  cg24399405    chr16 [189577, 189578]      * |     5420600      460327     Grn
             platform percentGC               sourceSeq probeType  probeStart
                <Rle> <numeric>          <DNAStringSet>     <Rle> <character>
  cg11876012     BOTH      0.36 TTTGTTACCT...CTGAATAGCG        cg      101638
  cg14820573     BOTH      0.44 CGTCAGTCTT...TGTTGTGGGA        cg      102073
  cg14747225     BOTH      0.54 AACAGCAAGT...TGAGAGATCG        cg      102976
  cg11653271     BOTH      0.64 CGCTCCCGGC...GGTCACTGCA        cg      103723
  cg16003913     BOTH      0.62 AAAAGGCCTT...GTGGGAGACG        cg      127072
  cg24399405     BOTH      0.44 GTTTAATTTA...CACTGCCTCG        cg      189577
                probeEnd probeTarget
             <character>   <numeric>
  cg11876012      101687      101686
  cg14820573      102122      102121
  cg14747225      103025      103024
  cg11653271      103772      103723
  cg16003913      127121      127072
  cg24399405      189626      189577
  -------
  seqinfo: 24 sequences from hg19 genome
>
ADD COMMENTlink written 3.4 years ago by James W. MacDonald52k
Answer: Common probes between 27K and 450 chip
0
gravatar for Adrian Johnson
3.4 years ago by
Adrian Johnson330 wrote:

Thank you very much. 

ADD COMMENTlink written 3.4 years ago by Adrian Johnson330
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