CNV.create_anno: CNV.create_anno

In conumee: Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Description

Create annotations for CNV analysis.

Usage

CNV.create_anno(bin_minprobes = 15, bin_minsize = 50000,
  bin_maxsize = 5000000, array_type = "450k", chrXY = FALSE,
  exclude_regions = NULL, detail_regions = NULL)

Arguments

bin_minprobes	numeric. Minimum number of probes per bin. Bins are interatively merged with neighboring bin until minimum number is reached.
bin_minsize	numeric. Minimum size of a bin.
bin_maxsize	numeric. Maximum size of a bin. Merged bins that are larger are filtered out.
array_type	character. One of 450k, EPIC, or overlap. Defaults to 450k.
chrXY	logical. Should chromosome X and Y be included in the analysis?
exclude_regions	GRanges object or path to bed file containing genomic regions to be excluded.
detail_regions	GRanges object or path to bed file containing genomic regions to be examined in detail.

Details

This function collects all annotations required for CNV analysis using Illumina 450k or EPIC arrays. The output CNV.anno object is not editable. Rerun CNV.create_anno to change parameters.

Value

CNV.anno object.

Author(s)

Volker Hovestadt [e-mail]

Examples

# create annotation object
anno <- CNV.create_anno()
anno

conumee documentation built on Nov. 8, 2020, 6 p.m.