sv_deletions: Creates a StructuralVariant object

In cancer-genomics/trellis: Somatic structural variant analysis

Creates a StructuralVariant object

Description

Creates a StructuralVariant object encapsulating information on deletions, including the genomic intervals, proper and improper read pairs in the vicinity, and a classification for the type of deletion based on the preprocessed estimates of read depth and the improper read pair alignments.

Usage

sv_deletions(preprocess, gr_filters, param = DeletionParam())

Arguments

preprocess	a list of preprocessing summaries (see preprocessData)
gr_filters	a GRanges object of germline filters. If the function is called without specifying this argument then a default set of germline filters will be applied from svfilters.hg19 if the genome slot in preprocess is set to "hg19" or svfilters.hg18 if genome is set to "hg18".
param	a DeletionParam object

Details

Note: proper read pairs near a candidate deletion are randomly sampled to reduce the size of the object. For reproducibility, set a seed prior to running this function.

Value

a StructuralVariant object

See Also

preprocessData

Examples

data(pdata)
pdata$bam.file <- system.file("extdata", "cgov44t_revised.bam", package="svbams")
sv_deletions(pdata)

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.