mpMap: Multi-parent RIL genetic analysis
Version 1.14

Tools for constructing linkage maps, reconstructing haplotypes, estimating linkage disequilibrium and QTL mapping in multi-parent RIL designs (e.g. MAGIC)

AuthorEmma Huang
Date of publication2012-06-06 05:59:03
MaintainerEmma Huang <Emma.Huang@csiro.au>
LicenseGPL-2
Version1.14
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("mpMap")

Getting started

Package overview

Popular man pages

add3pt: Add markers to a framework map using 3-point likelihoods
findqtl2: Detect a second QTL in a QTL profile from (composite)...
mpadd: Add markers onto an existing 'mpcross' object
mpIM: (Composite) Interval Mapping for QTL detection in...
mpprob: Compute founder probabilities for multi-parent crosses
plot.mpprob: Plot summary of founder probabilities and haplotype blocks
qtlmap: Select markers in a region around QTL
See all...

All man pages Function index File listing

Man pages

add3pt: Add markers to a framework map using 3-point likelihoods
cleanmap: Clean map for use in QTL mappin
clean.mpcross: Check data format and compute summary statistics for...
compare_orders: Compare potential orders for linkage groups
computemap: Computes map distances
fillmiss: Fill in missing values for an mpcross object
findqtl2: Detect a second QTL in a QTL profile from (composite)...
fit: Fit a full model including all QTL and effects from base...
mapcomp-all: Functions for comparison of two map orders
maporder: Helper function to ensure that mpcross objects are in map...
mpadd: Add markers onto an existing 'mpcross' object
mpcalcld: Calculate linkage disequilibrium between all pairs of markers
mpcross: Multi-parent cross object
mpestrf: Estimate pairwise recombination fractions between markers
mpgroup: Group markers into linkage groups given 2-pt recombination...
mpIM: (Composite) Interval Mapping for QTL detection in...
mp-mapdist: Conversion between recombination fractions (R) and map...
mpMap-internal: Internal mpMap functions
mpMap-output: Output mpcross objects to other file formats
mpMap-package: Genetic analysis in multi-parent crosses
mporder: Order markers within linkage groups
mpprob: Compute founder probabilities for multi-parent crosses
nai: Count how many generations of advanced intercross are in a...
plotlink.map: Plots linkage maps
plot.mpcross: Plot summary of mpcross object
plot.mpprob: Plot summary of founder probabilities and haplotype blocks
plot.mpqtl: Plot output from interval mapping with detected QTL
qtlmap: Select markers in a region around QTL
read.mpcross: Construct mpcross objects from datafiles
sim.mpcross: Simulate data from multi-parent designs
sim.mpped: Generate pedigrees from multi-parent designs
sim.sigthr: Simulate a significance threshold for (composite) interval...
subset.mpcross: Subset mpcross object
subset.mpprob: Subset mpprob object
summary.mpcross: Summary of mpcross object
summary.mpprob: Summary of mpprob object
summary.mpqtl: Summary of mpqtl object
supportinterval: Calculate support interval for detected QTL

Functions

CR_calcLD Man page Source code
CR_cross Man page Source code
CR_estrf Man page Source code
CR_gen_geno Man page Source code
add3pt Man page Source code
calc.genoprob2 Source code
calcmpprob Man page Source code
check_ped Man page Source code
check_qtl Man page Source code
cintern Man page Source code
clean.mpcross Man page Source code
cleanmap Man page Source code
cleanrf Man page Source code
combine_chr Man page Source code
combine_ibd Man page Source code
combine_ld Source code
combine_rf Man page Source code
compare_orders Man page Source code
compute.bnld Source code
compute_bnrf Man page Source code
computemap Man page Source code
convertped Man page Source code
fill Man page Source code
fillmiss Man page Source code
findqtl2 Man page Source code
fit Man page Source code
fit.mpqtl Man page Source code
gen4ped Man page Source code
gen8ped Man page Source code
generate_error Man page Source code
generate_obs Man page Source code
generate_pheno Man page Source code
getpval Man page Source code
haldaneR2X Man page Source code
haldaneX2R Man page Source code
kosambiR2X Man page Source code
kosambiX2R Man page Source code
mapcomp Man page Source code
maporder Man page Source code
mp.mapdist Man page
mpIM Man page Source code
mpMap Man page
mpMap-package Man page
mpadd Man page Source code
mpcalcld Man page Source code
mpcross Man page Source code
mpcross.object Man page
mpestrf Man page Source code
mpgroup Man page Source code
mporder Man page Source code
mpprob Man page Source code
mpsegrat Man page Source code
nai Man page Source code
plot.mapcomp Man page Source code
plot.mpcross Man page Source code
plot.mpprob Man page Source code
plot.mpqtl Man page Source code
plotlink.map Man page Source code
print.mapcomp Source code
print.mpcross Man page Source code
print.mpprob Man page Source code
print.mpqtl Source code
qtlmap Man page Source code
read.mpcross Man page Source code
reorgRIgenoprob Man page Source code
scan3pt Man page
sim.mpcross Man page Source code
sim.mpped Man page Source code
sim.sigthr Man page Source code
subset.mpcross Man page Source code
subset.mpprob Man page Source code
summary.mapcomp Man page Source code
summary.mpcross Man page Source code
summary.mpprob Man page Source code
summary.mpqtl Man page Source code
supportinterval Man page Source code
wald.test.asreml Man page Source code
write.mpcross Man page Source code
write2cross Man page Source code
write2happy Man page Source code

Files

MD5
TODO
src
src/sim.c
src/rngs.h
src/rngs.c
src/qsort.c
src/pf.c
src/mpMap.h
src/founderprob.c
src/calcLD.c
src/all.c
src/add3pt.c
src/3ptscan.c
R
R/waldTests.R
R/supportinterval.R
R/summary.mpqtl.R
R/summary.mpprob.R
R/summary.mpcross.R
R/subset.mpprob.R
R/subset.mpcross.R
R/sim.sigthr.R
R/sim.mpped.R
R/sim.mpcross.R
R/reorgRIgenoprob2.R
R/read.mpcross.R
R/qtlmap.R
R/print.mpqtl.R
R/print.mpprob.R
R/print.mpcross.R
R/print.mapcomp.R
R/plotlink.map.R
R/plot.mpqtl.R
R/plot.mpprob.R
R/plot.mpcross.R
R/nai.R
R/mpsegrat.R
R/mpprob.R
R/mporder.R
R/mpMap-output.R
R/mpIM.R
R/mpgroup.R
R/mpestrf.R
R/mpcross.R
R/mpcalcld.R
R/mpadd.R
R/mp-mapdist.R
R/maporder.R
R/mapcomp.R
R/getpval.R
R/generate-pheno.R
R/generate-obs.R
R/generate-error.R
R/gen8ped.R
R/gen4ped.R
R/fit.mpqtl.R
R/findqtl2.R
R/fillmiss.R
R/fill.R
R/CR-gen-geno.R
R/CR-estrf.R
R/CR-cross.R
R/CR-calcLD.R
R/convertped.R
R/computemap.R
R/compute-bnrf.R
R/compute-bnld.R
R/compare-orders.R
R/combine-rf.R
R/combine-ld.R
R/combine-ibd.R
R/combine-chr.R
R/cleanrf.R
R/cleanmap.R
R/clean.mpcross.R
R/check-QTL.R
R/check-ped.R
R/calcmpprob.R
R/calc.genoprob2.R
R/add3pt.R
NEWS
NAMESPACE
man
man/supportinterval.Rd
man/summary.mpqtl.Rd
man/summary.mpprob.Rd
man/summary.mpcross.Rd
man/subset.mpprob.Rd
man/subset.mpcross.Rd
man/sim.sigthr.Rd
man/sim.mpped.Rd
man/sim.mpcross.Rd
man/read.mpcross.Rd
man/qtlmap.Rd
man/plotlink.map.Rd
man/plot.mpqtl.Rd
man/plot.mpprob.Rd
man/plot.mpcross.Rd
man/nai.Rd
man/mpprob.Rd
man/mporder.Rd
man/mpMap-package.Rd
man/mpMap-output.Rd
man/mpMap-internal.Rd
man/mpIM.Rd
man/mpgroup.Rd
man/mpestrf.Rd
man/mpcross.Rd
man/mpcalcld.Rd
man/mpadd.Rd
man/mp-mapdist.Rd
man/maporder.Rd
man/mapcomp-all.Rd
man/fit.Rd
man/findqtl2.Rd
man/fillmiss.Rd
man/computemap.Rd
man/compare_orders.Rd
man/cleanmap.Rd
man/clean.mpcross.Rd
man/add3pt.Rd
inst
inst/CITATION
DESCRIPTION
mpMap documentation built on May 19, 2017, 12:16 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.