findExcluded: Excluded individuals and pairings in a DVI dataset

Description

Analysing exclusions is often an efficient way to reduce large DVI datasets. A pairing V = M is excluded if it implies (too many) genetic inconsistencies. The function findExcluded() identifies and removes (i) victim samples with too many inconsistencies against all missing persons, (ii) missing persons with too many inconsistencies against all victim samples, and (iii) inconsistent pairings among the remaining.

Usage

findExcluded(
  dvi,
  maxIncomp = 2,
  pairings = NULL,
  ignoreSex = FALSE,
  verbose = TRUE
)
exclusionMatrix(dvi, pairings = NULL, ignoreSex = FALSE)

Value

A list with the following entries:

exclusionMatrix: A matrix showing the number of inconsistencies for each pair (or NA if the pairing was not considered)
excluded: A list of three character vectors:
- sample: victim samples excluded against all missing persons
- missing: missing persons excluded against all victims
- fam: families in which all missing members are excluded against all victim samples
dviReduced: A reduced version of dvi, where the excluded elements are removed, and the pairings are updated.
summary: A list of data frames PM and AM, summarising the excluded individuals.

Arguments

dvi: A dviData() object.
maxIncomp: An integer. A pairing is excluded if the number of incompatible markers exceeds this.
pairings: A list of possible pairings for each victim. By default, dvi$pairings is used, or, if this is NULL, generatePairings(dvi, ignoreSex).
ignoreSex: A logical, by default: FALSE.
verbose: A logical, by default TRUE.

Details

The main calculation in findExcluded() is done by exclusionMatrix(), which records number of incompatible markers of each pairwise comparison.

Examples

Run this code

# \donttest{
e = findExcluded(icmp)
e$summary
e$exclusionMatrix

# The exclusion matrix can also be computed directly:
exclusionMatrix(icmp)

# Inspect a particular pair: M4 vs V4
forrel::findExclusions(icmp$am, id = "M4", candidate = icmp$pm$V4)

# Plot one of the incompatible markers
plotDVI(icmp, pm = 4, marker ="D7S820")
# }