conseq: Construct a consensus sequence

In DKMS-LSL/dr2s: Dual redundant reference sequencing

Description

Construct a consensus sequence

Usage

conseq(
  x,
  name = "conseq",
  type = c("prob", "ambig", "simple"),
  threshold = NULL,
  suppressAllGaps = FALSE,
  suppressInsGaps = TRUE,
  gapThreshold = NULL,
  columnOccupancy = 0.4,
  ...
)

Arguments

x	pileup object.
name	Name for consensus sequence.
type	One of "prob", "ambig" or "simple".
threshold	If type = "ambig", threshold to call an ambiguous consensus call.
suppressAllGaps	If type = "prob" or type = "ambig", suppress all gaps from consensus calling irrespective of the frequency of the gap.
suppressInsGaps	If type = "prob", suppress gaps at insertion position from consensus calling based on columnOccupancy.
columnOccupancy	Minimum occupancy (1 - fraction of gap) below which bases at insertion position are excluded from from consensus calling.
...	Additional arguments.

Value

A BStringSet object with a metadata list containing the slots:

zscore

freq

ambigs

insertions

deletions

consmat

Examples

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DKMS-LSL/dr2s documentation built on March 14, 2021, 2:46 p.m.