Test enrichment of one signature in another signature's ranked scores

Treats significant features from signature B as a feature set and tests whether their scores in signature A differ from the remaining ranked scores in signature A using a two-sample Kolmogorov-Smirnov test.

Usage

signatureSetKsTest(
  conn_handler = NULL,
  signature_id_a = NULL,
  signature_name_a = NULL,
  signature_id_b = NULL,
  signature_name_b = NULL,
  omic_signature_a = NULL,
  omic_signature_b = NULL,
  feature_col = "feature_name",
  score_col = "score",
  alternative = c("two.sided", "greater", "less"),
  verbose = TRUE
)

Arguments

conn_handler

An R object obtained from SigRepo::newConnHandler(). Required unless omic_signature_a and omic_signature_b are supplied.

signature_id_a

Database ID for signature A.

signature_name_a

Name for signature A.

signature_id_b

Database ID for signature B.

signature_name_b

Name for signature B.

omic_signature_a

Optional OmicSignature object containing the ranked scores. Scores are taken from omic_signature_a$difexp by default.

omic_signature_b

Optional OmicSignature object containing the significant feature set. Features are taken from omic_signature_b$signature.

feature_col

Column containing feature names. Defaults to "feature_name".

score_col

Column containing feature scores. Defaults to "score".

alternative

Alternative hypothesis passed to stats::ks.test().

verbose

Logical; whether or not to print diagnostic messages while retrieving signatures. Defaults to TRUE.

Value

A list containing the KS test result, feature counts, and ranked score table for signature A.