# Pedigree Functions

## Documentation for package ‘Pedixplorer’ version 1.5.5

- 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_server | Create the server logic for the ped_shiny application
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
ped_ui | Create the user interface for the ped_shiny application
plink_to_pedigree | Import from .fam file or .ped file
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