consensusConcordants: Generate a Consensus list of Targets *[Stable]*

In AliSajid/drugfindR: Investigate iLINCS for candidate repurposable drugs

Generate a Consensus list of Targets

Description

This function takes a list of (optionally split) concordance dataframes and returns a ranked list of gene or drug targets that have been chose for their maximal similarity to the signature

Usage

consensusConcordants(..., paired = FALSE, cutoff = 0.321, cellLine = NULL)

Arguments

...	One or Two (see paired) Data Frames with the concordants
paired	Logical indicating whether you split the dataframes by up and down regulated in prior analysis
cutoff	A similarity cutoff value. Defaults to 0.321
cellLine	A character vector of Cell Lines you are interested in.

Value

A tibble with the filtered and deduplicated results

Examples

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

# Get concordant gene knockdown signatures
concordantSignatures <- getConcordants(kdSignature, ilincsLibrary = "KD")

# Get the consensus list of signatures with defaults
consensus <- consensusConcordants(concordantSignatures)

# Get the consensus list of signatures with a different cutoff
consensus <- consensusConcordants(concordantSignatures,
    cutoff = 0.5
)

# Get the consensus list of signatures with a specified cell lines
consensus <- consensusConcordants(concordantSignatures,
    cellLine = c("A549", "MCF7")
)

# Doing a paired analysis
filteredUp <- filterSignature(kdSignature,
    direction = "up", threshold = 0.5
)
filteredDown <- filterSignature(kdSignature,
    direction = "down", threshold = -0.5
)

concordants_up <- getConcordants(filteredUp, ilincsLibrary = "KD")
concordants_down <- getConcordants(filteredDown, ilincsLibrary = "KD")

consensus <- consensusConcordants(concordants_up,
    concordants_down,
    paired = TRUE
)

AliSajid/drugfindR documentation built on Dec. 19, 2024, 7:30 p.m.