getAllCor | R Documentation |
getAllResiduals
and a phenotype paths vector made with tree2Paths
or char2Paths
Computes the association statistics between RER from getAllResiduals
and a phenotype paths vector made with tree2Paths
or char2Paths
getAllCor(
RERmat,
charP,
method = "auto",
min.sp = 10,
min.pos = 2,
winsorizeRER = NULL,
winsorizetrait = NULL,
weighted = F
)
RERmat |
RER matrix returned by |
charP |
phenotype vector returned by |
method |
Method used to compute correlations. Accepts the same arguments as |
min.sp |
Minimum number of species that must be present for a gene |
min.pos |
Minimum number of species that must be present in the foreground (non-zero phenotype values) |
winsorizeRER |
Winsorize RER values before computing Pearson correlation. winsorizeRER=3 will set the 3 most extreme RER values at each end of each row to the value closest to 0. |
winsorizetrait |
Winsorize trait values before computing Pearson correlation. winsorizetrait=3 will set the 3 most extreme trait values at each end to the value closest to 0. |
weighted |
perform weighted correlation. This option needs to be set if the clade weights computed in |
A list object with correlation values, p-values, and the number of data points used for each tree
winsorize is in terms of number of observations at each end, NOT quantiles
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