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

View source: R/investigateSignature.R

investigateSignatureR Documentation

Investigate a given DGE dataset [Experimental]

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

TRUE

CogDisResLab/drugfindR documentation built on June 15, 2024, 9:30 p.m.