conumee (version 1.4.2)

CNV.create_anno: CNV.create_anno

Description

Create annotations for CNV analysis.

Usage

CNV.create_anno(bin_minprobes = 15, bin_minsize = 50000, bin_maxsize = 5e+06, 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.

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.

Value

CNV.anno object.

Details

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

Examples

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