findExcluded {dvir} | R Documentation |
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.
findExcluded(
dvi,
maxIncomp = 2,
pairings = NULL,
ignoreSex = FALSE,
verbose = TRUE
)
exclusionMatrix(dvi, pairings = NULL, ignoreSex = FALSE)
dvi |
A |
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,
|
ignoreSex |
A logical, by default: FALSE. |
verbose |
A logical, by default TRUE. |
The main calculation in findExcluded()
is done by exclusionMatrix()
,
which records number of incompatible markers of each pairwise comparison.
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.
findUndisputed()
. See also forrel::findExclusions()
for analysis
of a specific pairwise comparison.
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")