[BioC] pd.mapping250k.sty package: featureSet:fragment_length

Zhu, Julie Julie.Zhu at umassmed.edu
Fri Sep 17 15:53:46 CEST 2010


Could someone please tell me whether the fragment_length in the featureSet
of pd.mapping250k.sty is the fragment_length of the sample? Are there
documentations available for looking up the meanings of each field?

Some rows have NAs for most the fields even though the allele information is
known, is this expected?

Thanks so much for your help!

con = db(pd.mapping250k.sty)
dbListFields(con, "featureSet")
 [1] "fsetid"          "man_fsetid"      "dbsnp_rs_id"     "chrom"
 [5] "physical_pos"    "strand"          "cytoband"        "allele_a"
 [9] "allele_b"        "gene_assoc"      "fragment_length" "dbsnp"
[13] "cnv" 

dbGetQuery(con, "select * from featureSet order by fsetid desc limit 2")
  fsetid    man_fsetid dbsnp_rs_id chrom physical_pos strand cytoband
allele_a allele_b
1 238378 SNP_A-4301986   rs6989223     8      5214036      -    p23.2
A        G
2 238377 SNP_A-2291495  rs11644392  <NA>           NA   <NA>     <NA>
A        G
  fragment_length dbsnp
1            1667     0
2              NA    NA

Best regards,


R version 2.11.1 (2010-05-31)

[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] pd.mapping250k.sty_1.0.0 RSQLite_0.9-2            DBI_0.2-5
[4] oligo_1.12.2             oligoClasses_1.10.0      Biobase_2.8.0
[7] affxparser_1.20.0

loaded via a namespace (and not attached):
[1] affyio_1.16.0         Biostrings_2.16.9     IRanges_1.6.11
[5] splines_2.11.1        tools_2.11.1

More information about the Bioconductor mailing list