Man pages for caitiecollins/treeWAS
Run phylogenetic tree-based GWAS

asrAncestral state reconstruction
assoc.testRun a test of association between SNPs and a phenotype.
coalescent.simSimulate a tree, phenotype, and genetic data.
coalescent.tree.simShort one-phrase description.
fwd.coalescent.simShort one-phrase description.
fwd.phen.simSimulate a phenotype, from root to tips.
fwd.snp.simShort one-phrase description.
get.ancestral.parsAncestral sequence reconstruction via parsimony
get.assoc.scoresGet significant SNPs, according to a given test of...
get.binary.snpsReduce a genetic data matrix to only necessary columns.
get.fitch.n.mtsCaclulate parsimony scores.
get.original.loci'(read.CFML+)' Get original sequence positions of polymorphic...
get.score3Short one-phrase description.
get.sig.snpsGet significant SNPs, according to a given test of...
get.tip.orderGet the order of the tip labels of a phylogenetic tree as...
get.unique.matrixGet unique rows/columns of a matrix with an index vector.
ggplotbgMimic ggplot2 Background
heatmap.DNAbinShort one-phrase description.
keepFirstNTruncate to keep only the _first_ N characters.
keepLastNTruncate to keep only the _last_ N characters.
manhattan.plotManhattan Plot
memfreeGet the current amount of available memory.
phen.simShort one-phrase description.
plot.phenPlot the states of a phenotype or genotype along a...
plot.prob.phenPlot the probability of association, given 'p' and...
plot.sig.snpsPlot null distribution and significant sites.
print.treeWASPrint 'treeWAS' output.
read.CFMLConvert ClonalFrameML output.
removeFirstNTruncate to remove all of the _first_ N characters.
removeLastNTruncate to remove all of the _last_ N characters.
selectBiallelicSNPShort one-phrase description.
set.argsSet a list of arguments.
simTestSimulation Testing.
simultaneous.testShort one-phrase description.
simultaneous.test.epiTest for association between genetic loci with Score 2.
snp.simShort one-phrase description.
snp.sim.QAternative SNPs simulation fn.
subsequent.testShort one-phrase description.
table.matrixCross-tabulate the rows or columns of a matrix.
terminal.testShort one-phrase description.
terminal.test.epiTest for epistasis between genetic loci with Score 1.
tree.reconstructShort one-phrase description.
treeWASPhylogenetic tree-based GWAS for microbes.
write.treeWASWrite 'treeWAS' output to a CSV file.
caitiecollins/treeWAS documentation built on April 19, 2019, 4:08 a.m.