Pedigree Functions

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Documentation for package ‘Pedixplorer’ version 1.3.1

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

Help Pages

A B C D E F G H I K L M N P R S U misc

Pedixplorer-package

The Pedixplorer package for pedigree data

-- A --

adopted	Ped object
adopted-method	Ped object
adopted<-	Ped object
adopted<--method	Ped object
affected	Ped object
affected-method	Ped object
affected<-	Ped object
affected<--method	Ped object
align	Align a Pedigree object
align-method	Align a Pedigree object
alignped1	Alignment first routine
alignped2	Alignment second routine
alignped3	Alignment third routine
alignped4	Alignment fourth routine
as.data.frame-method	Ped object
as.data.frame-method	Rel object
as.list-method	Hints object
as.list-method	Ped object
as.list-method	Pedigree object
as.list-method	Rel object
as.list-method	Scales object
asymptomatic	Ped object
asymptomatic-method	Ped object
asymptomatic<-	Ped object
asymptomatic<--method	Ped object
auto_hint	Initial hint for a Pedigree alignment
auto_hint-method	Initial hint for a Pedigree alignment
avail	Ped object
avail-method	Ped object
avail<-	Ped object
avail<--method	Ped object

-- B --

best_hint	Best hint for a Pedigree alignment
best_hint-method	Best hint for a Pedigree alignment
bit_size	Bit size of a Pedigree
bit_size-method	Bit size of a Pedigree
border	Scales object
border-method	Pedigree object
border-method	Scales object
border<-	Scales object
border<--method	Pedigree object
border<--method	Scales object

-- C --

carrier	Ped object
carrier-method	Ped object
carrier<-	Ped object
carrier<--method	Ped object
code	Rel object
code-method	Rel object
consultand	Ped object
consultand-method	Ped object
consultand<-	Ped object
consultand<--method	Ped object

-- D --

dadid	Ped object
dadid-method	Ped object
dadid<-	Ped object
dadid<--method	Ped object
dateofbirth	Ped object
dateofbirth-method	Ped object
dateofbirth<-	Ped object
dateofbirth<--method	Ped object
dateofdeath	Ped object
dateofdeath-method	Ped object
dateofdeath<-	Ped object
dateofdeath<--method	Ped object
deceased	Ped object
deceased-method	Ped object
deceased<-	Ped object
deceased<--method	Ped object

-- E --

evaluated	Ped object
evaluated-method	Ped object
evaluated<-	Ped object
evaluated<--method	Ped object

-- F --

famid	Ped object
famid-method	Ped object
famid-method	Rel object
famid<-	Ped object
famid<--method	Ped object
famid<--method	Rel object
family_infos_table	Affection and availability information table
fertility	Ped object
fertility-method	Ped object
fertility<-	Ped object
fertility<--method	Ped object
fill	Scales object
fill-method	Pedigree object
fill-method	Scales object
fill<-	Scales object
fill<--method	Pedigree object
fill<--method	Scales object
find_avail_affected	Find single affected and available individual from a Pedigree
find_avail_affected-method	Find single affected and available individual from a Pedigree
find_avail_noninform	Find uninformative but available subject
find_avail_noninform-method	Find uninformative but available subject
find_unavailable	Find unavailable subjects in a Pedigree
find_unavailable-method	Find unavailable subjects in a Pedigree
fix_parents	Fix parents relationship and gender
fix_parents-method	Fix parents relationship and gender

-- G --

generate_colors	Process the filling and border colors based on affection and availability
generate_colors-method	Process the filling and border colors based on affection and availability

-- H --

Hints	Hints object
hints	Pedigree object
Hints-class	Hints object
Hints-method	Hints object
hints-method	Pedigree object
hints<-	Pedigree object
hints<--method	Pedigree object
horder	Hints object
horder-method	Hints object
horder-method	Pedigree object
horder<-	Hints object
horder<--method	Hints object
horder<--method	Pedigree object

-- I --

ibd_matrix	IBD matrix
id	Ped object
id-method	Ped object
id1	Rel object
id1-method	Rel object
id2	Rel object
id2-method	Rel object
id<-	Ped object
id<--method	Ped object
isinf	Ped object
isinf-method	Ped object
isinf<-	Ped object
isinf<--method	Ped object
is_informative	Find informative individuals
is_informative-method	Find informative individuals
is_parent	Are individuals parents
is_parent-method	Are individuals parents

-- K --

kin	Ped object
kin-method	Ped object
kin<-	Ped object
kin<--method	Ped object
kindepth	Individual's depth in a pedigree
kindepth-method	Individual's depth in a pedigree
kinship	Kinship matrix
kinship-method	Kinship matrix

-- L --

length-method

Pedigree object

-- M --

make_famid	Compute family id
make_famid-method	Compute family id
mcols-method	Pedigree object
mcols<--method	Ped object
mcols<--method	Pedigree object
minnbreast	Minnesota Breast Cancer Study
min_dist_inf	Minimum distance to the informative individuals
min_dist_inf-method	Minimum distance to the informative individuals
miscarriage	Ped object
miscarriage-method	Ped object
miscarriage<-	Ped object
miscarriage<--method	Ped object
momid	Ped object
momid-method	Ped object
momid<-	Ped object
momid<--method	Ped object

-- N --

norm_ped	Normalise a Ped object dataframe
norm_rel	Normalise a Rel object dataframe
num_child	Number of childs
num_child-method	Number of childs

-- P --

parent_of	Get parents of individuals
parent_of-method	Get parents of individuals
Ped	Ped object
ped	Pedigree object
Ped-class	Ped object
Ped-method	Ped object
ped-method	Pedigree object
ped<-	Pedigree object
ped<--method	Pedigree object
Pedigree	Pedigree object
Pedigree-class	Pedigree object
Pedigree-method	Pedigree object
Pedixplorer	The Pedixplorer package for pedigree data
ped_shiny	Run Pedixplorer Shiny application
ped_to_legdf	Create plotting legend data frame from a Pedigree
ped_to_legdf-method	Create plotting legend data frame from a Pedigree
ped_to_plotdf	Create plotting data frame from a Pedigree
ped_to_plotdf-method	Create plotting data frame from a Pedigree
plot,Pedigree	Plot Pedigrees
plot-method	Plot Pedigrees
plot.Pedigree	Plot Pedigrees
plot_fromdf	Create a plot from a data.frame
proband	Ped object
proband-method	Ped object
proband<-	Ped object
proband<--method	Ped object

-- R --

Rel	Rel object
rel	Pedigree object
Rel-class	Rel object
Rel-method	Rel object
rel-method	Pedigree object
rel<-	Pedigree object
rel<--method	Pedigree object
relped	Relped data

-- S --

sampleped	Sampleped data
Scales	Scales object
scales	Pedigree object
Scales-class	Scales object
Scales-method	Scales object
scales-method	Pedigree object
scales<-	Pedigree object
scales<--method	Pedigree object
sex	Ped object
sex-method	Ped object
sex<-	Ped object
sex<--method	Ped object
show-method	Ped object
show-method	Pedigree object
show-method	Rel object
shrink	Shrink Pedigree object
shrink-method	Shrink Pedigree object
spouse	Hints object
spouse-method	Hints object
spouse-method	Pedigree object
spouse<-	Pedigree object
spouse<--method	Hints object
spouse<--method	Pedigree object
subset-method	Hints object
subset-method	Ped object
subset-method	Pedigree object
subset-method	Rel object
summary-method	Ped object
summary-method	Pedigree object
summary-method	Rel object

-- U --

unrelated	Find Unrelated subjects
unrelated-method	Find Unrelated subjects
upd_famid	Update family prefix in individuals id
upd_famid-method	Update family prefix in individuals id
useful	Ped object
useful-method	Ped object
useful<-	Ped object
useful<--method	Ped object
useful_inds	Usefulness of individuals
useful_inds-method	Usefulness of individuals

-- misc --

[-method

Pedigree object