mpMap: Multi-parent RIL genetic analysis

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

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

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