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

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Documentation for package ‘MinimumDistance’ version 1.4.0

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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"'