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)

Install the latest version of this package by entering the following in R:
install.packages("mpMap")
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

Functions

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

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

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

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

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