list.responses.factor.minimal {netresponse} | R Documentation |
List significantly associated responses for all factors and levels in the given annotation matrix
list.responses.factor.minimal(annotation.df, groupings, method = "hypergeometric", min.size = 2, pth = Inf, verbose = TRUE, data = NULL, rounding = NULL)
annotation.df |
annotation data.frame with discrete factor levels, rows named by the samples |
groupings |
List of groupings. Each model should have a sample-cluster assignment matrix qofz, or a vector of cluster indices named by the samples. |
method |
method for enrichment calculation |
min.size |
minimum sample size for a response |
pth |
p-value threshold; applied to adjusted p-value |
verbose |
verbose |
data |
data (samples x features; or a vector in univariate case) |
rounding |
rounding digits |
A list with two elements: Table listing all associations between the factor levels and responses; multiple p-value adjustment method
Contact: Leo Lahti leo.lahti@iki.fi
See citation("netresponse")