View source: R/PermulationFuncs.R
getPermsContinuous | R Documentation |
Calculates permuted correlation and enrichment statistics
getPermsContinuous(
numperms,
traitvec,
RERmat,
annotlist,
trees,
mastertree,
calculateenrich = T,
type = "simperm",
winR = 3,
winT = 3,
method = "p",
min.pos = 0
)
numperms |
An integer number of permulations |
traitvec |
A named phenotype vector |
RERmat |
An RER matrix calculated using |
annotlist |
Pathway annotations |
trees |
treesObj from |
mastertree |
A rooted, fully dichotomous tree derived from the treesObj master tree from |
calculateenrich |
A boolean variable indicating if null permulation p-values for enrichment statistics |
type |
One of "simperm", "sim", or "perm" for permulations, simulations, or permutations, respectively |
winR |
Integer winzorization value for RERmat |
winT |
Integer winzorization value for trait |
method |
statistical method to use for correlations |
min.pos |
minimum foreground species - should be set to 0 |
A list object with enrichment statistics, correlation p-val, rho, and correlation effect size
winsorize is in terms of number of observations at each end, NOT quantiles
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