Test_Leaf {DYNATE} | R Documentation |
Test_Leaf The function is used to generate Leaf P-values for case-control study. Users can input the leaf information through argument struct_map. If there is not leaf information e.g. struct_map=NULL, Test_Leaf will automatically construct leaf. Argument thresh_val specifies the leaf size constructed from the function. When the argument Gmat_case and Gmat_ctrl is null, Test_Leaf will automatically generate those matrices.
Description
Test_Leaf The function is used to generate Leaf P-values for case-control study. Users can input the leaf information through argument struct_map. If there is not leaf information e.g. struct_map=NULL, Test_Leaf will automatically construct leaf. Argument thresh_val specifies the leaf size constructed from the function. When the argument Gmat_case and Gmat_ctrl is null, Test_Leaf will automatically generate those matrices.
Usage
Test_Leaf(snp_dat = NULL, thresh_val = 10, covars = NULL, teststat = "FET")
Arguments
snp_dat |
an optional data frame containing patients mutation information. If |
thresh_val |
a positive integer for leaf size. |
covars |
an optional vector about the name of covariates to be considered in the fitting process. Should be NULL (default) or a character vector. |
teststat |
the statistic used to derive p-value. Must be one of "FET" (default) or "score". |
Value
a dataframe of rejected leafs with snp information.
Examples
data("snp_dat")
# Set leaf size M
M <- 5
#Construct leaves and generate leaf p-value.
p.leaf <- Test_Leaf(snp_dat=snp_dat,thresh_val=M)
summary(p.leaf)