knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
radiator is maturing, but in order to make the package better, changes are inevitable. Experimental functions will change, argument names will change.
Below an example of recent changes that are all documented in NEWS and changelog.
DArT users:
filter_dart
: is now deprecated. Please use filter_rad
.tidy_dart
and tidy_silico_dart
: are now deprecated.
Please use read_dart
for all the 4 DArT files recognized by radiator.Missing data: visualization and imputations
Visualizing missing data and it's imputations requires special attention that fall
outside the scope of radiator.
Inside my package called grur, users
can visualize patterns of missingness associated with different variables
(lanes, chips, sequencers, populations, sample sites, reads/samples, homozygosity, etc).
Several Map-independent imputations of missing genotypes are available:
Random Forests (on-the-fly-imputations or predictive modeling),
Extreme Gradient Tree Boosting,
Strawman imputations (~ max/mean/mode: the most frequently observed, non-missing genotypes is used).
Imputations can be conducted overall samples or by populations/strata/grouping.
radiator::genomic_converter
is integrated with the imputation function of grur.
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