AmpliconViews: Makes an AmpliconViews object

In BIMSBbioinfo/AmpliconBiSeq: analyzing amplicon bisulfite sequencing data

Description

Makes an AmpliconViews object from qProject object from QuasR.

Usage

AmpliconViews(proj, range, tag = NULL, sampleNames, conv = NULL,
  exp.var = 80, noise.tol = "auto", example.size = 100,
  call.matrix = FALSE, verbose = FALSE)

Arguments

proj	qProject object from QuasR
range	GRanges object for the amplicon locations
tag	a character vector, containing a additional tags that describe the amplicons. The vector length should be same as range object.
sampleNames	sample name as character
conv	minimum conversion efficiency a numeric value between 0 and 100, reads below this conversion efficiency will be discarded
exp.var	percentage of reads explained by meta-methylation patterns. This helps to infer top meta-methylation patterns. If set to 90, meta-patterns are ranked by their cluster sizes, and patterns that attributes to 90 percent of the data are returned.
noise.tol	percentage of variation to be considered as noise. This usually corresponds to PCA components that explain small percentage of the data to be removed. If equals to 'auto', the noise is automatically removed by removing components that explain low amount of variation.
example.size	size of the example matrix returned. example matrix contains example reads from the experiment.
call.matrix	logical, default FALSE, if TRUE methylation call matrix that contains methylation calls per fragment are returned. This might result in a large AmpliconViews object, should be set to FALSE normally.

Value

returns an AmpliconViews-class object

Examples

# a=GRanges(seqnames=,range=IRanges() )
 # av=ampliconView(proj,range=a[2,],samp="amSeq",conv=80,exp.var=80,example.size=100)

BIMSBbioinfo/AmpliconBiSeq documentation built on May 5, 2019, 10:25 a.m.