mpMap: Multi-parent RIL genetic analysis

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

Author
Emma Huang
Date of publication
2012-06-06 05:59:03
Maintainer
Emma Huang <Emma.Huang@csiro.au>
License
GPL-2
Version
1.14

View on CRAN

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

Files in this package

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