showChipInfo

margin

logical, whether to display class information

with.classinfo

logical, whether to display sequence lengths below
the main output listing (e.g, chromsomes). Usually tidier when this is FALSE.

print.seqlengths

hidden arguments including: 'head.tail'; number of SNPs to display 
at start/end (only the head and tail are shown as these objects are generally
very large with >100K SNPs); 'up.to'; only SNPs at the start and end are generally
displayed, however this parameter specifies that when there are 


Returns a preview of a ChipInfo object to the console. This
is similar to a GRanges preview, but the seqlevels are hidden, the UCSC
build and chip name are displayed, start and end are merged to the virtual
label 'position' (as it's assume we are dealing with SNPs, not ranges), the strand
by default is hidden, and the integer codes for pass/fail in QCcodes() are 
displayed as 'pass' or 'fail', even though this is not how they are represented internally.
This is called by the default 'show' method for ChipInfo objects.


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.

showChipInfo: Display a ChipInfo object

Description

Usage

Arguments

Value

See Also