humarray (version 1.0.0)

chip.support: Retrieve current ChipInfo annotation object

Description

This function returns the current 'ChipInfo' annotation object, containing chromosome, id, position, strand, 'rs' id, allele 1, allele 2 for each SNP of a microarray chip, in either hg18 or hg19 (build 36/37) coordinates. Can also be used to update the current object to a new object. This package makes extensive use of this class of annotation object for the working microarray chip, e.g, default is ImmunoChip, but Metabochip is also built-in, and you can also load your own annotation if using a different chip. The class of the object used is 'ChipInfo' which is a GRanges object, modified to always have columns for A1, A2 (alleles), rs.id, and a quality control flag. The default display is tidier than GRanges, it has nice coersion to and frame data.frame and indexing by chromosome using [[n]] has been added, in addition to normal [i,j] indexing native to GRanges. A1 and A2 values are usually specific to each dataset so for immunochip you may need to manually update these values to reflect the allele coding in your own dataset.

Usage

chip.support(build = NULL, refresh = FALSE, alternate.file = NULL, warn.build = TRUE)

Arguments

build

character, either "hg18", "hg19" or "hg38". Will also accept build numbers, 36, 37 or 38.

refresh

logical, FALSE to just load whatever object is already in memory (except when first using a function in this package, there should be a ChipInfo object loaded), or TRUE to reload from the original source. For instance you may wish to do this when you want to use a different chip, different build, or if the annotation has been modifed via a manual correction).

alternate.file

character, name of an alternative RData file containing a ChipInfo object to use instead of the object found in getOption("chip.info"). This will replace the current ChipInfo object.

warn.build

logical, whether to warn if the 'build' argument does not match the current value of getOption("ucsc"). The default is to display this warning, but if you set this argument to FALSE this can be suppressed.

Value

returns the current ChipInfo object [S4]. This may be slow first time, but subsequent lookups should be much faster. Builds 36/38 are not stored explicitly so will take a little while to convert the first time, but subsequent lookups should be fast. To increase the speed save the object locally and use option(chip.info=) to set a custom path for future chip.support() calls [which are also made internally by many of the function in this package]. This is also the option to set if you want to add a ChipInfo object for a different chip, e.g, metabochip, exomechip, etc.

See Also

ChipInfo, build, rs.id, QCfail, convTo36, convTo37, A1, A2

Examples

chip.support() # shows the current ChipInfo object (default is 'ImmunoChip' build 37)
#/donttest{
chip.support(build=36) # gives warning as hg19 version is currently loaded
chip.support(build=36,refresh=TRUE)
getOption("chip.info") # shows the object is now saved in the tmp directory for subsequent calls
chip.support(build=38,refresh=TRUE)
#}