Package: lineup 0.46

lineup: 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. Broman et al. (2015) <doi:10.1534/g3.115.019778>.

Authors:Karl W Broman [aut, cre]

lineup_0.46.tar.gz
lineup_0.46.zip(r-4.7)lineup_0.46.zip(r-4.6)lineup_0.46.zip(r-4.5)
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lineup_0.46.tar.gz(r-4.7-arm64)lineup_0.46.tar.gz(r-4.7-x86_64)lineup_0.46.tar.gz(r-4.6-arm64)lineup_0.46.tar.gz(r-4.6-x86_64)
lineup_0.46.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lineup/json (API)

# Install 'lineup' in R:

install.packages('lineup', repos = c('https://kbroman.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kbroman/lineup/issues

Datasets:

expr1 - Example gene expression data
expr2 - Example gene expression data
f2cross - Example experimental cross data
genepos - Genomic positions of genes in simulated expression data
pmap - Physical map of markers

On CRAN:

6.28 score 4 stars 105 scripts 317 downloads 13 exports 3 dependencies

Last updated from:89f5167e37. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	153
linux-devel-x86_64	OK	150
source / vignettes	OK	225
linux-release-arm64	OK	147
linux-release-x86_64	OK	148
macos-release-arm64	OK	83
macos-release-x86_64	OK	225
macos-oldrel-arm64	OK	77
macos-oldrel-x86_64	OK	271
windows-devel	OK	100
windows-release	OK	91
windows-oldrel	OK	103
wasm-release	OK	119

Exports:calc.locallod combinedist corbetw2mat distee disteg find.gene.pseudomarker findCommonID fscale lineupversion omitdiag plot2dist plotEGclass pulldiag

Dependencies:class MASS qtl

R/lineup user guide

Example data | Lining up expression data | Lining up expression and genotype data | Conclusions

Rendered fromlineup.Rmdusingknitr::rmarkdown

Last update: 2026-07-02
Started: 2015-06-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate LOD score at physical position of each gene	calc.locallod
Combine distance matrices into a single such	combinedist
Calculate correlations between columns of two matrices	corbetw2mat
Calculate distance between two gene expression data sets	distee
Calculate distance between two gene expression data sets	disteg
Example gene expression data	expr-data expr1 expr2
Example experimental cross data	f2cross
Find nearest peudomarker to each gene	find.gene.pseudomarker
Find individuals in common between a cross and a phenotype matrix	findCommonID
Standardize the columns of a matrix	fscale
Genomic positions of genes in simulated expression data	genepos
Installed version of R/lineup	lineupversion
Replace the diagonal in a distance matrix with missing values	omitdiag
Plot summary of inter-individual distances	plot.lineupdist
Plot two sets of inter-individual distances against one another	plot2dist
Plot classifier of eQTL genotype from expression data	plotEGclass
Physical map of markers	pmap
Pull out the diagonal from a distance matrix	pulldiag
Subsetting distance matrix	subset.lineupdist [.lineupdist
Summarize inter-individual distances	summary.lineupdist