humarray-package: Simplify Analysis and Annotation of Human Microarray Datasets

Description Details Author(s) See Also Examples

Description

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.

Details

Package: humarray
Type: humarray
Version: 1.1
Date: 2017-01-02
License: GPL (>= 2)

This package helps to simplify common tasks in human genetics research, such as annotation lookup, conversion and labelling for GWAS analysis. Functions are provided that utilise GRanges, IRanges and data.frame (snpStats) objects for input and output. The new ChipInfo object, based on GRanges, once established, can provide seamless and automatic lookup for SNPs and their features within all functions, with no need to keep passing an object explicitly with each function call. By default, the annotation for immunoChip is built-in, but you can provide your own annotation for any chip to take its place. Intuitive wrappers are provided for annotation lookup (gene lists, exon ranges, cytobands, telomeres, etc) which take care of database lookup and download seamlessly in the background. Conversion between build 36 and 37 coordinates, with parameters required in most cases. New functions allow simple conversion between ensembl and HGNC gene labels, and chip specific ids to rs-ids for SNP-arrays. Simple function allow fast retrieval of chromosome and position for gene labels, karyotype bands or SNP-ids, or reverse lookup to see which features appear at, or nearest to a given location. There are randomisation functions to generate simulated GRanges and RangedData objects, lists of sample IDs and lists of SNP-ids.

List of functions ANNOTATION LOOKUP:

RANGED DATA:

CHIP SUPPORT:

Author(s)

Nicholas Cooper

Maintainer: Nicholas Cooper <njcooper@gmx.co.uk>

See Also

NCmisc ~~

Examples

1
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#' randomly generated GRanges object
rranges()

humarray documentation built on May 30, 2017, 4:36 a.m.