get_sig_feature_association: Calculate Association between Signature Exposures and Other...

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Calculate Association between Signature Exposures and Other Features

Description

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.

Usage

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,
  ...
)

Arguments

data	a data.frame contains signature exposures and other features
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 cols_to_features.
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 TRUE, print extra message.
...	other arguments passing to test functions, like cor.test.

Value

a list. For 'co' features, 'measure' means correlation coefficient. For 'ca' features, 'measure' means difference in means of signature exposure.

See Also

get_tidy_association

sigminer documentation built on May 29, 2024, 3:11 a.m.