What the Package Does (Title Case)

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Documentation for package ‘autohaplo’ version 0.1

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across.center.ld Drop markers which are not in LD with at least one other marker across the center position.
calc.ld Calculate linkage desiquilibrium and keep the resulting matrix in the SnpObject.
combine.snpObject Combines two snpObjects into one.
distance.filter Drop markers which are past a certain relative distance from the central position.
genotype.filter Filters the markers from a SnpObject based on their overall genotypes.
get.max.ld.across.center Determine the maximum LD between markers across the gene center.
get.min.interval Subset a snpObject based upon the IQR of markers and the max R^2.
ld.block Drop markers in perfect LD with adjacent markers, keeping only a single representative marker.
ld.block.each.side Perform LD clustering on either side of the gene.
marker.selection Applies all filters of the pipeline designed by Aurélie Tardivel.
marker.subset Subsets a snpObject by keeping only certain markers.
one.side.ld Drop markers which are not in LD with at least one other marker on their side of the gene divide.
parse.hapmap Parse a hapmap file.
plot.chromosome Generates a plot showing the position of markers along the chromosome.
plot.distance.distribution Plots a distribution of the distances between markers on either side of the gene.
plot.ld.distance Generates a plot showing the relationship between LD and distance between markers.
plot.ld.matrix Generates a tile plot of the LD of the given snpObject.
position.filter Drop markers based on the overall distribution of marker positions.
position.subset Subsets a snpObject by keeping only markers within a certain interval.
read.vcf Parse a vcf file.
snpObject.output Output both the hapmap/vcf export and the graphs.
split.snpObject Splits an snpObject in its 5' and 3' components relative to the gene.
write.hapmap Export an SnpObject into the hapmap format.
write.vcf Write VCF output