Pedigree Functions


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Documentation for package ‘Pedixplorer’ version 1.3.1

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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