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mpMap (version 1.14)

Multi-parent RIL genetic analysis

Description

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

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Version

Install

install.packages('mpMap')

Monthly Downloads

21

Version

1.14

License

GPL-2

Maintainer

Emma Huang

Last Published

June 6th, 2012

Functions in mpMap (1.14)

cleanmap

Clean map for use in QTL mappin
maporder

Helper function to ensure that mpcross objects are in map order
findqtl2

Detect a second QTL in a QTL profile from (composite) interval mapping
mapcomp

Functions for comparison of two map orders
plot.mpcross

Plot summary of mpcross object
write.mpcross

Output mpcross objects to other file formats
mpadd

Add markers onto an existing 'mpcross' object
fit

Fit a full model including all QTL and effects from base model
plot.mpqtl

Plot output from interval mapping with detected QTL
mpcalcld

Calculate linkage disequilibrium between all pairs of markers
subset.mpcross

Subset mpcross object
haldaneR2X

Conversion between recombination fractions (R) and map distance (X)
mpprob

Compute founder probabilities for multi-parent crosses
plotlink.map

Plots linkage maps
summary.mpqtl

Summary of mpqtl object
mpcross

Multi-parent cross object
mpgroup

Group markers into linkage groups given 2-pt recombination fraction estimates
computemap

Computes map distances
qtlmap

Select markers in a region around QTL
mpIM

(Composite) Interval Mapping for QTL detection in multi-parent crosses
fillmiss

Fill in missing values for an mpcross object
plot.mpprob

Plot summary of founder probabilities and haplotype blocks
sim.mpcross

Simulate data from multi-parent designs
read.mpcross

Construct mpcross objects from datafiles
mpMap-internal

Internal mpMap functions
supportinterval

Calculate support interval for detected QTL
compare_orders

Compare potential orders for linkage groups
clean.mpcross

Check data format and compute summary statistics for genotypes
summary.mpprob

Summary of mpprob object
summary.mpcross

Summary of mpcross object
sim.mpped

Generate pedigrees from multi-parent designs
add3pt

Add markers to a framework map using 3-point likelihoods
subset.mpprob

Subset mpprob object
mpMap-package

Genetic analysis in multi-parent crosses
mpestrf

Estimate pairwise recombination fractions between markers
mporder

Order markers within linkage groups
nai

Count how many generations of advanced intercross are in a pedigree
sim.sigthr

Simulate a significance threshold for (composite) interval mapping