Question: From rs IDs to NCBI dbSNP IDs
0
gravatar for anastasiya-terskih
4.6 years ago by
Russian Federation
anastasiya-terskih10 wrote:

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!

sift rsids dbsnp • 889 views
ADD COMMENTlink modified 4.6 years ago by James W. MacDonald50k • written 4.6 years ago by anastasiya-terskih10

dbSNP ids are rsids.  Please provide error messages or other indications of failure along with sessionInfo() result.

ADD REPLYlink written 4.6 years ago by Vincent J. Carey, Jr.6.3k

When I use rsids as  keys:

si<-select(SIFT.Hsapiens.dbSNP137, keys=rsid, cols=subst1)

, I can't find them in SIFT.Hsapiens.dbSNP137.  I have the message that there are not such keys in SIFT.Hsapiens.dbSNP137.

Here is the message fron manual:

 This package, SIFT.Hsapiens.dbSNP137, contains both SIFT and
PROVEAN scores. One notable difference between this and the previous SIFT database package is
that keys in SIFT.Hsapiens.dbSNP132 are rs IDs whereas in SIFT.Hsapiens.dbSNP137 they are
NCBI dbSNP IDs.

 

ADD REPLYlink written 4.6 years ago by anastasiya-terskih10
Answer: From rs IDs to NCBI dbSNP IDs
1
gravatar for James W. MacDonald
4.6 years ago by
United States
James W. MacDonald50k wrote:

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?

ADD COMMENTlink written 4.6 years ago by James W. MacDonald50k

Yes, it works!Thank you very much!
 

ADD REPLYlink written 4.6 years ago by anastasiya-terskih10
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