RearrangementParams-class: Parameter class for rearrangement analysis

In cancer-genomics/trellis: Somatic structural variant analysis

Parameter class for rearrangement analysis

Description

Some details about why we look for linked tag clusters.

Some details about why we look for linked tag clusters.

Usage

rpSeparation(object)

minNumberTagsPerCluster(object)

minClusterSize(object)

maxClusterSize(object)

minGapWidth(object)

percentModalType(object)

RearrangementParams(
  rp_separation = 10000,
  min_number_tags_per_cluster = 5,
  min_cluster_size = 115L,
  max_cluster_size = 5000L,
  min.gapwidth = 1000L,
  percent_modal_type = 0.9,
  percent_linking = 0.8
)

## S4 method for signature 'RearrangementParams'
rpSeparation(object)

## S4 method for signature 'RearrangementParams'
minNumberTagsPerCluster(object)

## S4 method for signature 'RearrangementParams'
minClusterSize(object)

## S4 method for signature 'RearrangementParams'
maxClusterSize(object)

## S4 method for signature 'RearrangementParams'
minGapWidth(object)

## S4 method for signature 'RearrangementParams'
percentModalType(object)

percentLinking(object)

RearrangementParams(
  rp_separation = 10000,
  min_number_tags_per_cluster = 5,
  min_cluster_size = 115L,
  max_cluster_size = 5000L,
  min.gapwidth = 1000L,
  percent_modal_type = 0.9,
  percent_linking = 0.8
)

rpSeparation(object)

minNumberTagsPerCluster(object)

minClusterSize(object)

maxClusterSize(object)

minGapWidth(object)

percentModalType(object)

## S4 method for signature 'RearrangementParams'
rpSeparation(object)

## S4 method for signature 'RearrangementParams'
minNumberTagsPerCluster(object)

## S4 method for signature 'RearrangementParams'
minClusterSize(object)

## S4 method for signature 'RearrangementParams'
maxClusterSize(object)

## S4 method for signature 'RearrangementParams'
minGapWidth(object)

## S4 method for signature 'RearrangementParams'
percentModalType(object)

percentLinking(object)

Arguments

object	a RearrangementParams object
rp_separation	length-one numeric vector indicating minimum separation of the first and last read of a pair
min_number_tags_per_cluster	length-one numeric vector indicating the minimum number of reads in a cluster and the minimum number of reads required to link two clusters
min_cluster_size	length-one numeric vector; the minimum size of a cluster of reads
max_cluster_size	length-one numeric vector; the maximum size of a cluster of reads
min.gapwidth	length-one numeric vector; reads with at most min.gapwidth separation between them are considered overlapping.
percent_modal_type	length-one numeric vector; the percentage of reads that must agree with the modal rearrangement type
percent_linking	length-one numeric vector; two linked tag clusters must be linked by at least this percentage of reads. See details

Details

A tag cluster is defined as follows:

(i) it must have at least <min_number_tags_per_cluster> reads

(ii) Provided (i) is TRUE, the cluster includes all improper reads with less than <min.gapwidth> separation

(iii) The size of a cluster is defined as the difference in the minimum basepair across all members and the maximum basepair across all members. The size of the cluster must be at least <min_cluster_size> and no bigger than <max_cluster_size>.

Having determined the type of rearrangment supported by each read pair for two linked clusters, we require that the modal rearrangement type be supported by at least <percent_modal_type>> read pairs.

A tag cluster is defined as follows:

(i) it must have at least <min_number_tags_per_cluster> reads

(ii) Provided (i) is TRUE, the cluster includes all improper reads with less than <min.gapwidth> separation

(iii) The size of a cluster is defined as the difference in the minimum basepair across all members and the maximum basepair across all members. The size of the cluster must be at least <min_cluster_size> and no bigger than <max_cluster_size>.

Having determined the type of rearrangment supported by each read pair for two linked clusters, we require that the modal rearrangement type be supported by at least <percent_modal_type>> read pairs.

Slots

rp_separation

length-one numeric vector

min_number_tags_per_cluster

length-one numeric vector

min_cluster_size

length-one numeric vector

max_cluster_size

length-one numeric vector

min.gapwidth

length-one numeric vector

percent_modal_type

length-one numeric vector

percent_linking

length-one numeric vector

rp_separation

length-one numeric vector

min_number_tags_per_cluster

length-one numeric vector

min_cluster_size

length-one numeric vector

max_cluster_size

length-one numeric vector

min.gapwidth

length-one numeric vector

percent_modal_type

length-one numeric vector

percent_linking

length-one numeric vector

Examples

## Default rearrangement parameters for whole genome sequence data
##  with 30x coverage
rp <- RearrangementParams()


## Default rearrangement parameters for whole genome sequence data
##  with 30x coverage
rp <- RearrangementParams()

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