Compare significant feature overlap between two signatures

Returns the number of significant features unique to signature A, unique to signature B, and shared by both signatures. Significant features are read from the signature table of each OmicSignature object retrieved from the SigRepo database. If you already have OmicSignature objects, pass them with omic_signature_a and omic_signature_b.

Usage

compareSignatureFeatures(
  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",
  plot = FALSE,
  label_a = NULL,
  label_b = NULL,
  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 R6 object for signature A.

omic_signature_b

Optional OmicSignature R6 object for signature B.

feature_col

Column containing feature names. Defaults to "feature_name".

plot

Logical; whether to draw a simple Venn diagram. Defaults to FALSE.

label_a

Label for signature A in the plot and output table.

label_b

Label for signature B in the plot and output table.

verbose

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

...

Additional arguments passed to plotSignatureOverlap() when plot = TRUE.

Value

A data frame with counts for features unique to A, overlapping, and unique to B.