DeletionParam-class: Parameter class for calling deletions
In cancer-genomics/trellis: Somatic structural variant analysis

DeletionParam-class

R Documentation

Parameter class for calling deletions

Description

Parameter class for calling deletions

Usage

DeletionParam(
  min_width = 2000,
  max_width = 2e+06,
  min_gapwidth = 10000,
  homozygous_thr = -3,
  hemizygous_thr = -0.7,
  tumor_purity = 1,
  min_RPs_in_hemizygous = 1,
  max_RPs_in_homozygous = 100,
  nflanking_hemizygous = 5L,
  nflanking_homozygous = 5L,
  maxRatioObservedToExpected = 2L,
  max_proportion_in_filter = 0.75,
  min_segmean_diff = -0.5,
  bam_seqlevels_style = "UCSC",
  remove_hemizygous = TRUE
)

bamSeqLevelsStyle(object)

homozygousThr(object)

hemizygousThr(object)

maximumWidth(object)

maximumProportionInFilter(object)

minSegmeanDiff(object)

maxRatioObservedToExpected(object)

minimumWidth(object)

minimumGapWidth(object)

minFlankingHemizygous(object)

minFlankingHomozygous(object)

minRPsHemizygous(object)

maxRPsHomozygous(object)

Arguments

`min_width`	length-one numeric vector indicating the minimum width of a CNV segment.
`max_width`	length-one numeric vector indicating the maximum width of a CNV segment.
`min_gapwidth`	length-one numeric vector used to reduce deletion calls. Provided that the segment means of adjacent deletions are qualitatively similar, two deletions less than min_gapwidth apart will be merged into a single CNV.
`homozygous_thr`	length-one numeric vector indicating the maximum log2 ratio expected for a homozygous deletion
`hemizygous_thr`	length-one numeric vector indicating the maximum log2 ratio expected for a hemizygous deletion
`tumor_purity`	length-one numeric vector in [0, 1]
`min_RPs_in_hemizygous`	length-one numeric vector indicating the minimum number of rearranged read pairs that can be spanned by a hemizygous deletion. [PARAMETER NOT USED]
`max_RPs_in_homozygous`	length-one numeric vector indicating the maximum number of read pairs allowed to be spanned by a homozygous deletion. [PARAMETER NOT USED]
`nflanking_hemizygous`	length-one numeric vector indicating the minimum number of rearranged RPs required for calling a hemizygous deletion with higher confidence. Hemizygous deletions with rearranged RPs are given higher priority over hemizygous deletions supported only by the tag density.
`nflanking_homozygous`	length-one numeric vector indicating the minimum number of rearranged RPs required for calling a homozygous deletion with higher confidence. Homozygous deletions with rearranged RPs are given higher priority over homozygous deletions supported only by the tag density.
`maxRatioObservedToExpected`	length-one numeric vector [IGNORED?]
`max_proportion_in_filter`	length-one numeric vector indicating the maximum proportion of a CNV that can be covered by one of the filters. The filters are germline CNV, low mappability, low GC / unassembled regions, and outliers observed in a bin for 2 or more normal samples.
`min_segmean_diff`	length one numeric vector indicating how much less the segment mean for a deletion must be relative to the median log ratio of bins encompassed in an interval surrounding the segment of length equal to 15 times the width of the deleted segment.
`bam_seqlevels_style`	character string indicating style of seqnames
`object`	a `DeletionParam`
`build`	length-1 character vector indicating genome build (must be hg18 or hg19)

Value

a DeletionParam object

Slots

homozygous_thr: length-one numeric vector indicating the maximum fold change expected for a homozygous deletion
hemizygous_thr: length-one numeric vector indicating the maximum fold change expected for a hemizygous deletion
min_width: length-one numeric vector indicating the minimum width of a CNV segment.
max_width: length-one numeric vector indicating the maximum width of a CNV segment.
min_gapwidth: length-one numeric vector used to reduce deletion calls. Provided that the segment means of adjacent deletions are qualitatively similar, two deletions less than min_gapwidth apart will be merged into a single CNV.
min_RPs_in_hemizygous: length-one numeric vector indicating the minimum number of rearranged read pairs that can be spanned by a hemizygous deletion. [PARAMETER NOT USED]
max_RPs_in_homozygous: length-one numeric vector indicating the maximum number of read pairs allowed to be spanned by a homozygous deletion. [PARAMETER NOT USED]
nflanking_hemizygous: length-one numeric vector indicating the minimum number of rearranged RPs required for calling a hemizygous deletion with higher confidence. Hemizygous deletions with rearranged RPs are given higher priority over hemizygous deletions supported only by the tag density.
nflanking_homozygous: length-one numeric vector indicating the minimum number of rearranged RPs required for calling a homozygous deletion with higher confidence. Homozygous deletions with rearranged RPs are given higher priority over homozygous deletions supported only by the tag density.
maxRatioObservedToExpected: length-one numeric vector [IGNORED?]
max_proportion_in_filter: length-one numeric vector indicating the maximum proportion of a CNV that can be covered by one of the filters. The filters are germline CNV, low mappability, low GC / unassembled regions, and outliers observed in a bin for 2 or more normal samples.
min_segmean_diff: length one numeric vector indicating how much less the segment mean for a deletion must be relative to the median log ratio of bins encompassed in an interval surrounding the segment of length equal to 15 times the width of the deleted segment.
bam_seqlevels_style: character string indicating style of seqnames
tumor_purity: estimated fraction of sequenced DNA that is tumor-derived
remove_hemizygous: whether to remove "hemizygous" calls ('hemizygous+' calls are not removed).