createGeneSignature: Create a user-defined gene signature

In YosefLab/VISION: Functional interpretation of single cell RNA-seq latent manifolds

Create a user-defined gene signature

Description

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.

Usage

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

## Not run: 
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)

## End(Not run)

YosefLab/VISION documentation built on June 14, 2024, 5:27 p.m.