getConcordants: Get Concordant Signatures from iLINCS *[Experimental]*

In CogDisResLab/drugfindR: Investigate iLINCS for candidate repurposable drugs

Get Concordant Signatures from iLINCS

Description

This function takes a full or filtered signature and gets concordant signatures from any of the 3 LINCS databases in iLINCS. This can get Overexpression, Knockdown or Chemical Perturbagen signatures.

Usage

getConcordants(signature, ilincsLibrary = "CP")

Arguments

signature	A data frame with the names of genes, their expression value and optionally their p-value
ilincsLibrary	The Library you want to search. Must be one of "OE", "KD" or "CP" for Overexpression, Knockdown or Chemical Perturbagens

Value

A tibble with the list of concordant and discordant signatures

Examples

# Get the L1000 signature for LINCSKD_28
kdSignature <- getSignature("LINCSKD_28")

# Get concordant gene knockdown signatures

concordant_signatures <- getConcordants(kdSignature, ilincsLibrary = "KD")

head(concordant_signatures)

CogDisResLab/drugfindR documentation built on June 22, 2024, 10:01 p.m.