Aligning rows or columns | Correlations between matrices | Correlations/distances between samples | Summarize correlations/distances | Identify sample mix-ups | Second-best samples | References
Package: lineup2 0.7-2
lineup2: Lining Up Two Sets of Measurements
Tools for detecting and correcting sample mix-ups between two sets of measurements, such as between gene expression data on two tissues. This is a revised version of the 'lineup' package, to be more general and not tied to the 'qtl' package.
Authors:
lineup2_0.7-2.tar.gz
lineup2_0.7-2.zip(r-4.7)lineup2_0.7-2.zip(r-4.6)lineup2_0.7-2.zip(r-4.5)
lineup2_0.7-2.tgz(r-4.6-x86_64)lineup2_0.7-2.tgz(r-4.6-arm64)lineup2_0.7-2.tgz(r-4.5-x86_64)lineup2_0.7-2.tgz(r-4.5-arm64)
lineup2_0.7-2.tar.gz(r-4.7-arm64)lineup2_0.7-2.tar.gz(r-4.7-x86_64)lineup2_0.7-2.tar.gz(r-4.6-arm64)lineup2_0.7-2.tar.gz(r-4.6-x86_64)
lineup2_0.7-2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lineup2/json (API)
| # Install 'lineup2' in R: |
| install.packages('lineup2', repos = c('https://kbroman.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kbroman/lineup2/issues
Datasets:
- lineup2ex - Example dataset for lineup2 package
Last updated from:13522606e5. Checks:13 OK. Indexed: yes.
A new build is currently in progress.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 164 | ||
| linux-devel-x86_64 | OK | 167 | ||
| source / vignettes | OK | 260 | ||
| linux-release-arm64 | OK | 160 | ||
| linux-release-x86_64 | OK | 168 | ||
| macos-release-arm64 | OK | 141 | ||
| macos-release-x86_64 | OK | 281 | ||
| macos-oldrel-arm64 | OK | 159 | ||
| macos-oldrel-x86_64 | OK | 461 | ||
| windows-devel | OK | 132 | ||
| windows-release | OK | 135 | ||
| windows-oldrel | OK | 132 | ||
| wasm-release | OK | 151 |
Exports:align_matrix_colsalign_matrix_rowscorr_betw_matricesdist_betw_arraysdist_betw_matricesget_2ndbestget_bestget_nonselfget_problemsget_selfhist_self_nonselfplot_samplewhich_2ndbestwhich_best
Dependencies:Rcpp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Align the columns of two matrices | align_matrix_cols |
| Align the rows of two matrices | align_matrix_rows |
| Calculate correlations between columns of two matrices | corr_betw_matrices |
| Distance between rows of two arrays | dist_betw_arrays |
| Distance between rows of two matrices | dist_betw_matrices |
| Get 2nd-smallest distance for each individual | get_2ndbest |
| Get smallest distance for each individual | get_best |
| Get self-nonself distances | get_nonself |
| Summarize potential problems in a distance matrix | get_problems |
| Get self-self distance | get_self |
| Plot histograms of self-self and self-nonself distances | hist_self_nonself |
| Example dataset for lineup2 package | lineup2ex |
| Plot the distances for a given sample | plot_sample |
| Determine which individual has 2nd-smallest distance to each individual | which_2ndbest |
| Determine which individual has smallest distance to each individual | which_best |
