mqmplot.heatmap
(Package: qtl) :
Heatmap of a genome of MQM scan on multiple phenotypes
Plotting routine to display a heatmap of results obtained from a multiple-QTL model on multiple phenotypes (the output of mqmscanall)
● Data Source:
CranContrib
● Keywords: hplot
● Alias: mqmplot.heatmap
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replacemap.scantwo
(Package: qtl) :
Replace the genetic map in QTL mapping results with an alternate map
Replace the positions of LOD scores in output from scantwo with values based on an alternative map (such as a physical map), with pseudomarker locations determined by linear interpolation.
● Data Source:
CranContrib
● Keywords: manip
● Alias: replacemap.scantwo
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orderMarkers
(Package: qtl) :
Find an initial order for markers within chromosomes
Establish initial orders for markers within chromosomes by a greedy algorithm, adding one marker at a time with locations of previous markers fixed, in the position giving the miniminum number of obligate crossovers.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: orderMarkers
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add.threshold
(Package: qtl) :
Add significance threshold to plot
Add a significance threshold to a plot created by plot.scanone), using the permutation results.
● Data Source:
CranContrib
● Keywords: hplot
● Alias: add.threshold
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scanonevar
(Package: qtl) :
Genome scan for QTL affecting mean and/or variance
Genome scan with a single QTL model for loci that can affect the variance as well as the mean.
● Data Source:
CranContrib
● Keywords: models
● Alias: scanonevar
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mqmtestnormal
(Package: qtl) :
Shapiro normality test used for MQM
Wraps a shapiro's normality test from the nortest package. This function is used in MQM to test the normality of the trait under investigation
● Data Source:
CranContrib
● Keywords: utilities
● Alias: mqmtestnormal
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nmar
(Package: qtl) :
Determine the numbers of markers on each chromosome
Determine the number of markers on each chromosome in a cross or map object.
● Data Source:
CranContrib
● Keywords: print
● Alias: nmar
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mqmplot.permutations
(Package: qtl) :
Plot results from mqmpermutation
Plotting routine to display the results from a permutation QTL scan. (the output of mqmpermutation)
● Data Source:
CranContrib
● Keywords: hplot
● Alias: mqmplot.permutations
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plot.scantwoperm
(Package: qtl) :
Plot permutation results for a 2d, 2-QTL genome scan
Plot a histogram of the permutation results from a two-dimensional, two-QTL genome scan.
● Data Source:
CranContrib
● Keywords: hplot
● Alias: plot.scantwoperm
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pull.geno
(Package: qtl) :
Pull out the genotype data from a cross
Pull out the genotype data from a cross object, as a single big matrix.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: pull.geno
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