CNV.create_anno2: Create Conumee annotation for CNV analysis.

In markgene/yamatCN: Yet Another Methylation Array Toolkit Copy Number Analysis

Description

Rewrite CNV.create_anno() to be compatible with ilm10b3.hg19 and ilm10b4.hg19 annotation of EPIC array. I also change the default array type to EPIC.

Usage

CNV.create_anno2(array_type = "EPIC", array_anno = "ilm10b4.hg19",
  bin_minprobes = 15, bin_minsize = 50000, bin_maxsize = 5e+06,
  chrXY = FALSE, exclude_regions = NULL, detail_regions = NULL)

Arguments

array_type	A character scalar. One of "450k", "EPIC", or "overlap". Defaults to "EPIC".
array_anno	A character scalar. One of "ilm10b2.hg19", "ilm10b3.hg19", "ilm10b4.hg19". Only valid when array_type is set to "EPIC". Default to "ilm10b4.hg19".
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.

Details

This function collects all annotations required for CNV analysis using Illumina 450k or EPIC/850K arrays. I rewrite the function so that it can generate the annotation for the list of probes specified by the experiments.

Value

An object of CNV.anno-class.

Note

I have tested with EPIC ilm10b4.hg19, but not other arrays and annotations.

markgene/yamatCN documentation built on Dec. 7, 2019, 4:36 a.m.