R/get_sig_feature_association.R
get_sig_feature_association.Rd
Association of signature exposures with other features will be performed using one of two procedures: for a continuous association variable (including ordinal variable), correaltion is performed; for a binary association variable, samples will be divided into two groups and Mann-Whitney U-test is performed to test for differences in signature exposure medians between the two groups. See get_tidy_association for cleaning association result.
get_sig_feature_association( data, cols_to_sigs, cols_to_features, type = "ca", method_co = c("spearman", "pearson", "kendall"), method_ca = stats::wilcox.test, min_n = 0.01, verbose = FALSE, ... )
data | a |
---|---|
cols_to_sigs | colnames for signature exposure |
cols_to_features | colnames for other features |
type | a character vector containing 'ca' for categorical variable and 'co' for continuous variable,
it must have the same length as |
method_co | method for continuous variable, default is "spearman", could also be "pearson" and "kendall". |
method_ca | method for categorical variable, default is "wilcox.test" |
min_n | a minimal fraction (e.g. 0.01) or a integer number (e.g. 10) for filtering some variables with few positive events. Default is 0.01. |
verbose | if |
... | other arguments passing to test functions, like |
a list
. For 'co' features, 'measure' means correlation coefficient.
For 'ca' features, 'measure' means difference in means of signature exposure.