chipId

chipId,ChipInfo-method


Returns the chip-ids for the chip object, e.g, "imm_1_898835", etc
Only if these are annotated internally, or else a vector of NAs
Note that the main purpose of this is because sometimes chip-ids
do not satisfy conditions to be an R column/row name, e.g, start
with a number, illegal characters, etc. So this allows certain
functions to return the actual chip names that would match the 
official manifest. These will largely be the same as the rownames,
but the rownames will always be valid R column names, converted from
the original using clean.snp.ids() [internal function]


Utilises GRanges, data.frame or IRanges objects. Integrates gene annotation for ImmunoChip (or your custom chip) with function calls. Intuitive wrappers for annotation lookup (gene lists, exon ranges, etc) and conversion (e.g, between build 36 and 37 coordinates). Conversion between ensembl and HGNC gene ids, chip ids to rs-ids for SNP-arrays. Retrieval of chromosome and position for gene, band or SNP-ids, or reverse lookup. Simulation functions for ranges objects.

chipId: Access chip-ids for ChipInfo

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