filterSignature: Filter the L1000 Signature *[Experimental]*

In CogDisResLab/drugfindR: Investigate iLINCS for candidate repurposable drugs

Filter the L1000 Signature

Description

This function filters the L1000 Signature to a given threshold, identifying up-regulated or down-regulated or both up- and down-regulated genes

Usage

filterSignature(signature, direction = "any", threshold = NULL, prop = NULL)

Arguments

signature	A dataframe with the L1000 signature
direction	Direction to filter to. Must be one of "up", "down" or "any". Defaults to "any"
threshold	A Log Fold-Change Threshold to filter at. This can either be a single value or a vector of two values. If a single value is given, then it is assumed to be a symmetric threshold. If two values are given, then the first value is the down-regulated threshold and the second value is the up-regulated threshold. Cannot be specified with prop
prop	A proportion of genes to take from top and bottom. Cannot be specified with threshold

Value

a tibble with the filtered L1000 Signature

Examples

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

# Filter signature by a specific threshold
filteredSignature <- filterSignature(kdSignature, threshold = 0.5)

# Filter signature by a proportion

filteredSignature <- filterSignature(kdSignature, prop = 0.1)

# Filter Signature to up-regulated genes only by a threshold

filteredSignature <- filterSignature(kdSignature,
    direction = "up", threshold = 0.5
)

# Filter the signature using differing thresholds for up and
# down-regulated genes

filteredSignature <- filterSignature(kdSignature,
    threshold = c(-0.75, 0.5)
)

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