Create a user-defined gene signature

Typical usage of VISION involes providing a location to a ".gmt" signature file from which VISION automatically creates Signature objects. However, using the createGeneSignature method, users may programmatically define signatures from within R.

createGeneSignature(name, sigData, metadata = "")

Arguments

name

the name of the signature

sigData

a named vector where the names correspond to genes in the data and the values are either `1.0` for up-regulated (or positive) genes, and `-1.0` for down-regulated (negtive) genes. For an unsigned signature use 1.0 for all values.

metadata

metadata that is relevent to the signature. [Default:NULL]

Value

a Signature object

Examples

if (FALSE) {
sig1 <- createGeneSignature(
           name = "CD8 Markers",
           sigData = c(CD8A=1, CD8B=1, GZMK=1, GZMB=1,
                       GZMH=1, GZMA=1, GNLY=1, DUSP2=1,
                       EOMES=1, TBX21=1, PRMD1=1, PRF1=1,
                       IFNG=1)
       )

cc_sigs <- "path/to/cell_cycle.gmt"

sigs <- c(sig1, cc_sigs)

vis <- Vision(data = expMat, signatures = sigs)
}