# A package for de novo CNV detection in case-parent trios

## Documentation for package ‘MinimumDistance’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D F G I L M N O P S T U X misc

## -- A --

allNames | Class '"TrioSetList"'
allNames-method | Container for storing pedigree information
allNames-method | Class '"TrioSet"'
allNames-method | Class '"TrioSetList"'
annotatedDataFrameFrom-method | Methods for creating AnnotatedDataFrame objects
annotatedDataFrameFrom-methods | Methods for creating AnnotatedDataFrame objects
annotation-method | Class '"TrioSetList"'

## -- B --

baf | Class '"TrioSetList"'
baf-method | Class '"TrioSet"'
baf-method | Class '"TrioSetList"'
baf<- | Class '"TrioSet"'
baf<--method | Class '"TrioSet"'

## -- C --

calculateMindist | Compute the minimum distance.
calculateMindist-method | Class '"TrioSet"'
calculateMindist-method | Compute the minimum distance.
callDenovoSegments | Posterior calling for segmented data.
coerce-method | Class '"TrioSet"'
coerce-method | Class '"TrioSetList"'
coerce-method | Methods for coercing objects from one class to another
concAtTop | Functions for assessing concordance
correspondingCall | Find overlapping ranges

## -- D --

dim-method | Container for storing pedigree information
dim-method | Class '"TrioSet"'
dims-method | Class '"TrioSetList"'
discAtTop | Functions for assessing concordance

## -- F --

fatherNames | Class '"TrioSetList"'
fatherNames-method | Container for storing pedigree information
fatherNames-method | Class '"TrioSet"'
fatherNames-method | Class '"TrioSetList"'
fatherNames<- | Class '"TrioSet"'
fatherNames<--method | Class '"TrioSet"'
fatherPhenoData | Extract phenotype data for parents in a trio.
fatherPhenoData-method | Class '"TrioSet"'
fatherPhenoData-method | Class '"TrioSetList"'
featureData-method | Class '"TrioSetList"'

## -- G --

gcSubtract | Generic function for GC correction

## -- I --

initialize-method | Container for storing pedigree information
initialize-method | Class '"TrioSet"'
initialize-method | Class '"TrioSetList"'
isDenovo | Indicator for whether a trio copy number state is a de novo copy number alteration.

## -- L --

length-method | Class '"TrioSetList"'
lrr-method | Class '"TrioSet"'
lrr-method | Class '"TrioSetList"'
lrr.segs | Objects containing segmented data
lrr<- | Class '"TrioSet"'
lrr<--method | Class '"TrioSet"'

## -- M --

mad2 | Methods for computing the minimum absolute distance.
mad2-method | Class '"TrioSetList"'
mad2-method | Methods for computing the minimum absolute distance.
MAP | Estimate the trio copy number for minimum distance segments
MAP-method | Class '"TrioSet"'
MAP-method | Class '"TrioSetList"'
map.segs | Objects containing segmented data
md.segs | Objects containing segmented data
mindist | Class '"TrioSet"'
mindist-method | Class '"TrioSet"'
mindist-method | Class '"TrioSetList"'
mindist<- | Class '"TrioSet"'
mindist<--method | Class '"TrioSet"'
mindist<--method | Class '"TrioSetList"'
motherNames | Class '"TrioSetList"'
motherNames-method | Container for storing pedigree information
motherNames-method | Class '"TrioSet"'
motherNames-method | Class '"TrioSetList"'
motherPhenoData | Extract phenotype data for parents in a trio.
motherPhenoData-method | Class '"TrioSet"'
motherPhenoData-method | Class '"TrioSetList"'

## -- N --

narrowRanges | Adjust breakpoints from segmentation inward
ncol-method | Class '"TrioSet"'
ncol-method | Class '"TrioSetList"'
nrow-method | Class '"TrioSetList"'

## -- O --

offspringNames | Class '"TrioSetList"'
offspringNames-method | Container for storing pedigree information
offspringNames-method | Class '"TrioSet"'
offspringNames-method | Class '"TrioSetList"'
offspringPhenoData | Class '"TrioSet"'
offspringPhenoData-method | Class '"TrioSet"'
offspringPhenoData-method | Class '"TrioSetList"'
order-method | Class '"TrioSet"'
order-method | Class '"TrioSetList"'

## -- P --

Pedigree | Constructor for Pedigree class
pedigree | Class '"TrioSetList"'
Pedigree-class | Container for storing pedigree information
pedigree-method | Class '"TrioSet"'
pedigree-method | Class '"TrioSetList"'
phenoData-method | Class '"TrioSetList"'

## -- S --

sampleNames-method | Class '"TrioSetList"'
segment2 | Wrapper for segment function in package DNAcopy
segment2-method | Wrapper for segment function in package DNAcopy
stack-method | Class '"TrioSetList"'
stackRangedDataList | Stack a list of RangedDataCBS objects.

## -- T --

trios | Class '"TrioSetList"'
trios-method | Container for storing pedigree information
trios-method | Class '"TrioSet"'
trios-method | Class '"TrioSetList"'
TrioSet | Constructor for TrioSet objects.
TrioSet-class | Class '"TrioSet"'
TrioSetList | Constructs and object of class 'TrioSetList'
trioSetList | An example of a 'TrioSetList' object
TrioSetList-class | Class '"TrioSetList"'
trioSetListExample | An example of a 'TrioSetList' object
TrioSetListLD | Constructor for TrioSetList class for large data

## -- U --

updateObject-method | Class '"TrioSet"'
updateObject-method | Class '"TrioSetList"'

## -- X --

xypanelTrio | Panel function for a lattice-style plot of log R ratios, BAFs, and the minimum distance for a trio.
xyplot-method | Class '"TrioSet"'
xyplotTrio | Function for plotting log R ratios, BAFs, and the minimum distance for a trio using lattice.

## -- misc --

$-method | Class '"TrioSetList"'
[-method | Container for storing pedigree information
[-method | Class '"TrioSet"'
[-method | Class '"TrioSetList"'
[[-method | Class '"TrioSetList"'