Hello!Could you help me, please.

I need to use SIFT.Hsapiens.dbSNP137 instead of  SIFT.Hsapiens.dbSNP132.

I have the list of rsIDs to use SIFT.Hsapiens.dbSNP132, but keys in SIFT.Hsapiens.dbSNP137 are NCBI dbSNP IDs. I don't know how i can find NCBI dbSNP IDs.

Actually I used predictCoding() to get information about nucleotide substitutions (output is vcf_mod1) but I had no rsID in my output so I overlaped the GRanges I've got from predictCoding() with the positition in
the SNPloc package:

> library(SNPlocs.Hsapiens.dbSNP.20100427)

> ch1gr <-getSNPlocs("ch1", as.GRanges=TRUE)

> hits <- findOverlaps(vcf_mod1, ch1gr)

> ch1gr[subjectHits(hits),]

> rsid <- paste0("rs", mcols(ch1gr[subjectHits(hits),])$RefSNP_id)

May be I can overlap some information from PredictCoding with another SNPloc package  that contains

NCBI dbSNP IDs?

Thank you!

I think what Vince was trying to point out to you is that rsIDs and dbSNP IDs are the same, once you strip off the rs part.

> rsids <- head(keys(SIFT.Hsapiens.dbSNP132), 50)
> old <- select(SIFT.Hsapiens.dbSNP132, keys = rsids)

> new <- select(SIFT.Hsapiens.dbSNP137, gsub("rs", "", rsids))
Warning message:
3 keys not found in PROVEAN database: 332 698 1882

> head(old)
   RSID PROTEINID AACHANGE    METHOD AA PREDICTION SCORE MEDIAN POSITIONSEQS
1  rs47 NP_056019    N583D BEST HITS  D  TOLERATED 0.640   1.49           77
2  rs47 NP_056019    N583D BEST HITS  N  TOLERATED 0.490   1.49           77
3  rs47 NP_056019    N583D  ALL HITS  D  TOLERATED  0.69   2.04           93
4  rs47 NP_056019    N583D  ALL HITS  N  TOLERATED  0.49   2.04           93
5 rs268 NP_000228    N318S BEST HITS  S  TOLERATED 0.350   2.01           94
6 rs268 NP_000228    N318S BEST HITS  N  TOLERATED 1.000   2.01           94
  TOTALSEQS
1       101
2       101
3        99
4        99
5        97
6        97

> head(new)
  DBSNPID        VARIANT       PROTEINID LENGTH STRAND     CODONCHANGE POS
1      47 7,11581121,T,C ENSP00000262042   1657      - GGA [A/G]AC TGC 583
2      47 7,11581121,T,C ENSP00000406482   1657      - GGA [A/G]AC TGC 583
3     268 8,19813529,A,G ENSP00000309757    475      + ATC A[A/G]T AAA 318
4     268 8,19813529,A,G ENSP00000438606    461      + ATC A[A/G]T AAA 304
5     268 8,19813529,A,G ENSP00000439407    275      + ATC A[A/G]T AAA 242
6     298 8,19816860,G,A ENSP00000309757    475      + ACC [G/A]TG GCC 370
  RESIDUEREF RESIDUEALT             TYPE PROVEANSCORE PROVEANPRED PROVEANNUMSEQ
1          N          D Single AA Change        0.206     Neutral           107
2          N          D Single AA Change        0.206     Neutral           107
3          N          S Single AA Change       -1.085     Neutral           243
4          N          S Single AA Change       -1.085     Neutral           243
5          N          S Single AA Change       -1.068     Neutral           216
6          V          M Single AA Change        0.495     Neutral           243
  PROVEANNUMCLUST SIFTSCORE  SIFTPRED SIFTMEDIAN SIFTNUMSEQ
1              30     0.633 Tolerated       2.86         80
2              30      0.63 Tolerated       2.85         81
3              30     0.253 Tolerated       2.82        189
4              30     0.258 Tolerated       2.84        202
5              30     0.235 Tolerated       2.86        209
6              30     0.219 Tolerated       2.82        183

Does that help?