investigateTarget: Investigate a Given Gene or Drug *[Stable]*

In CogDisResLab/drugfindR: Investigate iLINCS for candidate repurposable drugs

Investigate a Given Gene or Drug

Description

This function takes the name of a gene or a drug and a database to use to pull signatures from and then queries iLINCS to get concordant signatures

Usage

investigateTarget(
  target,
  inputLib,
  outputLib,
  filterThreshold = 0.85,
  similarityThreshold = 0.321,
  paired = TRUE,
  inputCellLines = NULL,
  outputCellLines = NULL
)

Arguments

target	The name of the gene or drug
inputLib	One of "OE", "KD" or "CP". Marks the database to use.
outputLib	One of "OE", "KD" or "CP". Marks the database to query.
filterThreshold	The Filtering threshold.
similarityThreshold	The Similarity Threshold
paired	Logical. Whether to query iLINCS separately for up and down regulated genes
inputCellLines	A character vector of cell lines to restrict our search for input signatures to.
outputCellLines	A character vetor of cell lines to restrict the output search to.

Value

A tibble with the the similarity scores and signature metadata

Examples

# Search the whole iLINCS database for top concordant signatures for an
# ABL2 knockdown signature

investigatedSignature <- investigateTarget("ABL2",
    inputLib = "KD",
    outputLib = "CP",
    filterThreshold = 0.5
)

CogDisResLab/drugfindR documentation built on Dec. 19, 2024, 8:18 p.m.