Tools for constructing linkage maps, reconstructing haplotypes, estimating linkage disequilibrium and QTL mapping in multi-parent RIL designs (e.g. MAGIC)
|Date of publication||2012-06-06 05:59:03|
|Maintainer||Emma Huang <Emma.Huang@csiro.au>|
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