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DESCRIPTION
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Package: Pedixplorer
Version: 1.1.5
Date: 2024-10-01
Title: Pedigree Functions
Authors@R: c(
person("Louis", "Le Nézet", email="[email protected]",
role=c("aut","cre","ctb"), comment = c(ORCID = "0009-0000-0202-2703")),
person("Jason", "Sinnwell", email="[email protected]", role="aut"),
person("Terry", "Therneau", role="aut"),
person("Daniel", "Schaid", role="ctb"),
person("Elizabeth", "Atkinson", role="ctb"))
Depends:
R (>= 4.3.0)
Imports:
graphics,
stats,
methods,
ggplot2,
utils,
grDevices,
stringr,
plyr,
dplyr,
tidyr,
quadprog,
Matrix,
S4Vectors,
shiny,
readxl,
shinyWidgets,
htmlwidgets,
DT,
gridExtra,
data.table,
plotly,
colourpicker,
shinytoastr,
scales,
shinycssloaders
Description: Routines to handle family data with a Pedigree object. The initial
purpose was to create correlation structures that describe family
relationships such as kinship and identity-by-descent, which can be used to
model family data in mixed effects models, such as in the coxme function.
Also includes a tool for Pedigree drawing which is focused on producing
compact layouts without intervention. Recent additions include utilities to
trim the Pedigree object with various criteria, and kinship for the X
chromosome.
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Suggests:
diffviewer,
testthat (>= 3.0.0),
vdiffr,
rmarkdown,
BiocStyle,
knitr,
withr,
qpdf,
shinytest2,
covr,
devtools,
R.devices,
usethis,
magick
Config/testthat/edition: 3
biocViews: Software, DataRepresentation, Genetics, GraphAndNetwork, Visualization
BugReports: https://github.com/LouisLeNezet/Pedixplorer/issues
URL: https://louislenezet.github.io/Pedixplorer/
BiocType: Software
Collate:
'AllValidity.R'
'AllClass.R'
'kindepth.R'
'kinship.R'
'utils.R'
'AllConstructor.R'
'AllAccessors.R'
'AllGeneric.R'
'Pedixplorer-package.R'
'alignped4.R'
'alignped3.R'
'alignped2.R'
'alignped1.R'
'auto_hint.R'
'align.R'
'app.R'
'app_color_picker.R'
'app_data_col_sel.R'
'app_data_download.R'
'app_data_import.R'
'app_utils.R'
'app_family_sel.R'
'app_health_sel.R'
'app_inf_sel.R'
'app_ped_avaf_infos.R'
'app_plot_download.R'
'app_plot_legend.R'
'app_plot_ped.R'
'app_server.R'
'app_ui.R'
'best_hint.R'
'bit_size.R'
'data.R'
'descendants.R'
'family_check.R'
'find_unavailable.R'
'find_avail_affected.R'
'find_avail_noninform.R'
'fix_parents.R'
'generate_aff_inds.R'
'generate_colors.R'
'ibd_matrix.R'
'is_informative.R'
'make_famid.R'
'min_dist_inf.R'
'norm_data.R'
'num_child.R'
'ped_to_legdf.R'
'ped_to_plotdf.R'
'plot_fct.R'
'plot_fromdf.R'
'plot_pedigree.R'
'shrink.R'
'unrelated.R'
'useful_inds.R'
LazyData: false