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,
...
)a data.frame contains signature exposures and other features
colnames for signature exposure
colnames for other features
a character vector containing 'ca' for categorical variable and 'co' for continuous variable,
it must have the same length as cols_to_features.
method for continuous variable, default is "spearman", could also be "pearson" and "kendall".
method for categorical variable, default is "wilcox.test"
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.
if TRUE, print extra message.
other arguments passing to test functions, like cor.test.
a list. For 'co' features, 'measure' means correlation coefficient.
For 'ca' features, 'measure' means difference in means of signature exposure.
Macintyre, Geoff, et al. "Copy number signatures and mutational processes in ovarian carcinoma." Nature genetics 50.9 (2018): 1262.