profileCombinations: Compute drug combination response signatures

In retriever: Generate Disease-Specific Response Signatures from the LINCS-L1000 Data

Description

Returns the average of every possible two response profile non-redundant combination from the input matrix

Usage

profileCombinations(responseProfiles)

Arguments

responseProfiles

A matrix of response profiles for drugs (rows are genes, columns are drugs)

Value

A matrix with genes in the rows and profiles combination in the columns. The values represent the expected transcriptional response of the cells (used as input of retriever) to a drug combination.

Examples

# Loading robust profiles across different breast cancer cell lines generated by retriever.
# BRCA <- retriever(cellLines = c('MDAMB231', 'MCF7', 'SKBR3', 'HS578T', 'BT20'))

  BRCA <- read.csv(system.file("BRCA.csv",package="retriever"), row.names = 1)
  dim(BRCA)
  # [1] 1001  125

# Computing response profiles combinations
  combinationsBRCA <- profileCombinations(BRCA)
  dim(combinationsBRCA)
  # [1] 1001 7750

retriever documentation built on Nov. 11, 2021, 9:06 a.m.