investigateSignature: Investigate a given DGE dataset *[Stable]*

In CogDisResLab/drugfindR: Investigate iLINCS for candidate repurposable drugs

Investigate a given DGE dataset

Description

This function takes a DGE Data frame and then finds concordant signatures to that. This generates an L1000 signature from the DGE dataset and then uploads that signature to iLINCS to find the relevant concordant (or discordant) signatures

Usage

investigateSignature(
  expr,
  outputLib,
  filterThreshold = NULL,
  filterProp = NULL,
  similarityThreshold = 0.2,
  paired = TRUE,
  outputCellLines = NULL,
  geneColumn = "Symbol",
  logfcColumn = "logFC",
  pvalColumn = "PValue",
  sourceName = "Input",
  sourceCellLine = "NA",
  sourceTime = "NA",
  sourceConcentration = "NA"
)

Arguments

expr	A dataframe that has differential gene expression analysis
outputLib	The library to search
filterThreshold	The Filtering threshold.
filterProp	The Filtering proportion.
similarityThreshold	The Similarity Threshold
paired	Logical. Whether to query iLINCS separately for up and down regulated genes
outputCellLines	A character vector of cell lines to restrict the output search to.
geneColumn	The name of the column that has gene symbols
logfcColumn	The name of the column that has log_2 fold-change values
pvalColumn	The name of the column that has p-values
sourceName	(Optional) An annotation column to identify the signature by name
sourceCellLine	(Optional) An annotation column to specify the cell line for the input data
sourceTime	(Optional) An annotation column to specify the time for the input data
sourceConcentration	(Optional) An annotation column to specify the concentration for the input data

Value

A tibble with the the similarity scores and signature metadata

Examples

# Investigate a signature

# Load and prepare the signature
inputSignature <- read.table(system.file("extdata",
    "dCovid_diffexp.tsv",
    package = "drugfindR"
), header = TRUE)


# Investigate the signature

investigatedSignature <- investigateSignature(inputSignature,
    outputLib = "CP",
    filterThreshold = 0.5,
    geneColumn = "hgnc_symbol",
    logfcColumn = "logFC",
    pvalColumn = "PValue"
)

CogDisResLab/drugfindR documentation built on Nov. 19, 2024, 4:17 p.m.