Package index • Pedixplorer

Pedixplorer

Pedixplorer a Bioconductor package to create, filter and draw pedigrees.

Pedixplorer Pedixplorer-package: The Pedixplorer package for pedigree data

Pedigree S4 object

The Pedigree object is a S4 class that contains the pedigree data.

Pedigree(): Pedigree object

Ped(<data.frame>) Ped(<character_OR_integer>): Ped object

Rel(<data.frame>) Rel(<character_OR_integer>): Rel object

Scales(): Scales object

Hints(): Hints object

Pedigree construction

How to fix pedigree data and normalize it

fix_parents(<character>) fix_parents(<data.frame>): Fix parents relationship and gender

norm_ped(): Normalise a Ped object dataframe

norm_rel(): Normalise a Rel object dataframe

plink_to_pedigree(): Import from .fam file or .ped file

Shiny app

The Pedixplorer package comes with a shiny app to interact with the Pedigree object.

ped_shiny(): Run Pedixplorer Shiny application

ped_server(): Create the server logic for the ped_shiny application

ped_ui: Create the user interface for the ped_shiny application

Pedigree drawing and legend

The Pedigree object can be drawn using the plot method.

plot(<Pedigree>,<missing>): Plot Pedigrees

ped_to_plotdf(<Pedigree>): Create plotting data frame from a Pedigree

ped_to_legdf(<Pedigree>): Create plotting legend data frame from a Pedigree

plot_fromdf(): Create a plot from a data.frame

generate_colors(<character>) generate_colors(<numeric>) generate_colors(<Pedigree>): Process the filling and border colors based on affection and availability

Pedigree informations

Informations about the pedigree.

kinship(<Ped>) kinship(<character>) kinship(<Pedigree>): Kinship matrix

ibd_matrix(): IBD matrix

num_child(<character_OR_integer>) num_child(<Pedigree>): Number of childs

is_informative(<character_OR_integer>) is_informative(<Ped>) is_informative(<Pedigree>): Find informative individuals

family_infos_table(): Affection and availability information table

unrelated(<Ped>) unrelated(<Pedigree>): Find Unrelated subjects

parent_of(<character_OR_integer>) parent_of(<Ped>) parent_of(<Pedigree>): Get parents of individuals

is_parent(<character_OR_integer>) is_parent(<Ped>): Are individuals parents

make_famid(<character>) make_famid(<Pedigree>): Compute family id

upd_famid(<character>,<ANY>) upd_famid(<Ped>,<character_OR_integer>) upd_famid(<Ped>,<missing>) upd_famid(<Rel>,<character_OR_integer>) upd_famid(<Rel>,<missing>) upd_famid(<Pedigree>,<character_OR_integer>) upd_famid(<Pedigree>,<missing>): Update family prefix in individuals id

Pedigree filtering

Filtering methods to select a subset of individuals in a pedigree.

useful_inds(<character>) useful_inds(<Pedigree>) useful_inds(<Ped>): Usefulness of individuals

min_dist_inf(<character>) min_dist_inf(<Pedigree>) min_dist_inf(<Ped>): Minimum distance to the informative individuals

shrink(<Pedigree>) shrink(<Ped>): Shrink Pedigree object

bit_size(<character_OR_integer>) bit_size(<Pedigree>) bit_size(<Ped>): Bit size of a Pedigree

find_avail_affected(<Ped>) find_avail_affected(<Pedigree>): Find single affected and available individual from a Pedigree

find_avail_noninform(<Ped>) find_avail_noninform(<Pedigree>): Find uninformative but available subject

find_unavailable(<Ped>) find_unavailable(<Pedigree>): Find unavailable subjects in a Pedigree

Pedigree datasets

Different datasets are available to test the package.

minnbreast: Minnesota Breast Cancer Study

sampleped: Sampleped data

relped: Relped data

Pedigree alignment

Alignment methods to organize graphical representation of pedigrees.

align(<Pedigree>): Align a Pedigree object

alignped1(): Alignment first routine

alignped2(): Alignment second routine

alignped3(): Alignment third routine

alignped4(): Alignment fourth routine

auto_hint(<Pedigree>): Initial hint for a Pedigree alignment

best_hint(<Pedigree>): Best hint for a Pedigree alignment

kindepth(<character_OR_integer>) kindepth(<Pedigree>) kindepth(<Ped>): Individual's depth in a pedigree