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.

Author
Karl W Broman <kbroman@biostat.wisc.edu>
Date of publication
2015-07-29 00:11:39
Maintainer
Karl W Broman <kbroman@biostat.wisc.edu>
License
GPL-3
Version
0.37-6
URLs

View on CRAN

Man pages

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

Files in this package

lineup
lineup/inst
lineup/inst/TODO.txt
lineup/inst/LICENSE.txt
lineup/inst/doc
lineup/inst/doc/lineup.R
lineup/inst/doc/lineup.Rmd
lineup/inst/doc/lineup.html
lineup/tests
lineup/tests/testthat.R
lineup/tests/testthat
lineup/tests/testthat/test-combinedist.R
lineup/tests/testthat/test-corbetw2mat.R
lineup/src
lineup/src/util.c
lineup/src/rmsd.c
lineup/src/propmismatch.c
lineup/src/fscale.h
lineup/src/propmismatch.h
lineup/src/util.h
lineup/src/rmsd.h
lineup/src/corbetw2mat.c
lineup/src/corbetw2mat.h
lineup/src/fscale.c
lineup/NAMESPACE
lineup/NEWS
lineup/data
lineup/data/pmap.rda
lineup/data/expr1.rda
lineup/data/genepos.rda
lineup/data/datalist
lineup/data/f2cross.rda
lineup/data/expr2.rda
lineup/R
lineup/R/disteg.R
lineup/R/f2cross-data.R
lineup/R/genepos-data.R
lineup/R/omitdiag.R
lineup/R/combinedist.R
lineup/R/corbetw2mat.R
lineup/R/plot.lineupdist.R
lineup/R/pmap-data.R
lineup/R/subset.lineupdist.R
lineup/R/find.gene.pseudomarker.R
lineup/R/findCommonID.R
lineup/R/plotEGclass.R
lineup/R/util.R
lineup/R/expr1-data.R
lineup/R/plot2dist.R
lineup/R/fscale.R
lineup/R/distee.R
lineup/R/summary.lineupdist.R
lineup/R/pulldiag.R
lineup/R/calc.locallod.R
lineup/vignettes
lineup/vignettes/lineup.Rmd
lineup/MD5
lineup/build
lineup/build/vignette.rds
lineup/DESCRIPTION
lineup/ChangeLog
lineup/man
lineup/man/calc.locallod.Rd
lineup/man/lineupversion.Rd
lineup/man/plot2dist.Rd
lineup/man/plot.lineupdist.Rd
lineup/man/pmap.Rd
lineup/man/omitdiag.Rd
lineup/man/expr-data.Rd
lineup/man/corbetw2mat.Rd
lineup/man/find.gene.pseudomarker.Rd
lineup/man/summary.lineupdist.Rd
lineup/man/subset.lineupdist.Rd
lineup/man/distee.Rd
lineup/man/f2cross.Rd
lineup/man/pulldiag.Rd
lineup/man/plotEGclass.Rd
lineup/man/combinedist.Rd
lineup/man/findCommonID.Rd
lineup/man/disteg.Rd
lineup/man/fscale.Rd
lineup/man/genepos.Rd