Skip to content

updates main functionality to columnar samples #30

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Feb 16, 2024
Merged

updates main functionality to columnar samples #30

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,21 +1,21 @@
Package: visualizationQualityControl
Version: 0.4.11
Version: 0.5.1
Title: Development of visualization methods for quality control
Description: Provides utilities useful quality control of
high-throughput -omics datasets.
Authors@R: c(person(given = c("Robert", "M"), family = "Flight", email
= "rflight79@gmail.com", role = c("aut", "cre")), person(given
= c("Hunter", "NB"), family = "Moseley", email =
"hunter.moseley@gmail.com", role = c("aut")))
Date: 2021-12-28
Date: 2024-02-15
Depends: R (>= 3.1.1)
biocViews:
Imports: ComplexHeatmap (>= 1.2.1), stats, dendsort, colorspace, dplyr,
ggplot2, broom, knitrProgressBar, magrittr, purrr
License: MIT + file LICENSE
VignetteBuilder: knitr
Suggests: testthat, knitr, rmarkdown, circlize, viridis, ICIKendallTau,
ggforce
Suggests: testthat, knitr, rmarkdown, circlize, viridis, ICIKendallTau
(>= 1.0.0), ggforce
RoxygenNote: 7.2.3
Encoding: UTF-8
LinkingTo: Rcpp
Expand Down
12 changes: 1 addition & 11 deletions NAMESPACE
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,25 +4,15 @@ export("%>%")
export(calc_sd_rsd)
export(calc_sd_rsd_nls)
export(calculate_fratio)
export(calculate_weights)
export(correspondence)
export(count_matching_features)
export(determine_outliers)
export(filter_non_zero_percentage)
export(generate_group_colors)
export(globally_it_weighted_pairwise_correlation)
export(information_volume)
export(keep_non_missing_percentage)
export(keep_non_zero_percentage)
export(locally_it_weighted_pairwise_correlation)
export(median_class_correlations)
export(median_correlations)
export(outlier_fraction)
export(pairwise_correlation)
export(pairwise_correlation_both0)
export(pairwise_correlation_counts)
export(pairwise_correlation_multicore)
export(pairwise_distance)
export(pairwise_nonzero)
export(similarity_reorder)
export(similarity_reorderbyclass)
export(split_groups)
Expand Down
13 changes: 12 additions & 1 deletion NEWS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,15 @@
# vsualizationQualityControl 0.4.11
# visualizationQualityControl 0.5.0

* Changed some functions to treat columns as samples and rows as features:
* `keep_non_zero_percentage`
* `summarize_data`
* `calculate_fratio`

* Added `keep_non_missing_percentage`, which allows using multiple values to represent missingnes.
* Made `summarize_data` handle possible missing values.
* Removed correlation calculation functions, those have been superseded by [ICIKendallTau](https://moseleybioinformaticslab.github.io/ICIKendallTau/).

# visualizationQualityControl 0.4.11

* Added a new argument `only_high` to `determine_outliers` to only look at the high end of the score distribution for outliers, as sometimes `boxplot.stats` will pick up outliers at the low end as well.

Expand Down
Loading