Convert from chip/rs-ids to manifest chip ID labels

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Description

Some SNP-ids aren't legal R row/column names. In order to match datafiles and store annotation as objects, this package converts SNP-names to sanitized versions if necessary, that are legal row/column names. This function converts from such 'legal' versions of the IDs back to the proper names, as per the chip manifest document (or whatever is stored in the chip.id field of the chip.support() object, accessible using chipId()).

Usage

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manifest(ids)

Arguments

ids

character, either a list of rs-ids or chip-ids. chip ids are preferable as they are unique, and rs.ids are not. Using this function is not recommended for rs.id lists that might have entries that map to multiple chip ids, because entries other than the first will be ignored. For such cases, use 'rs.to.id(manifest=TRUE,multi.list=TRUE,...)'.

Value

A character vector of SNP chip-ids matching the manifest format.

Author(s)

Nicholas Cooper nick.cooper@cimr.cam.ac.uk

See Also

id.to.rs, GENE.to.ENS, ENS.to.GENE

Examples

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  test.ids <- c("imm_1_898835","rs61733845","rs115005664","rs114582555",
      "chr1_20131940","chr1_20133829","rs150992667","rs138231315","rs111577708","rs187104718")
  manifest(c("chr1_20131940","ccc_1_67429655_A_G"))
  manifest(test.ids)  # even when some are rs-id, still works
  data.frame(rs.id=test.ids,legal.id=rs.to.id(test.ids),manifest.id=manifest(test.ids))

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