investigate_signature: Investigate a given DGE dataset

In AliSajid/DrugDiscoveryPanCan: Investigate Drug Targets for Kinase Therapies

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

investigate_signature(
  expr,
  output_lib,
  filter_threshold = 0.85,
  similarity_threshold = 0.321,
  paired = TRUE,
  output_cell_lines = NULL,
  discordant = FALSE,
  gene_column = "Symbol",
  logfc_column = "logFC",
  pval_column = "PValue",
  source_name = "Input",
  source_cell_line = "NA",
  source_time = "NA",
  source_concentration = "NA"
)

Arguments

expr	A dataframe that has differential gene expression analysis
output_lib	The library to search
filter_threshold	The Filtering threshold.
similarity_threshold	The Similarity Threshold
paired	Logical. Whether to query iLINCS separately for up and down regulated genes
output_cell_lines	A character vetor of cell lines to restrict the output search to.
discordant	Logical. Whether to look for discordant signatures
gene_column	The name of the column that has gene symbols
logfc_column	The name of the column that has log_2 fold-change values
pval_column	The name of the column that has p-values
source_name	(Optional) An annotation column to identify the signature by name
source_cell_line	(Optional) An annotation column to specify the cell line for the input data
source_time	(Optional) An annotation column to specify the time for the input data
source_concentration	(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

AliSajid/DrugDiscoveryPanCan documentation built on Feb. 4, 2021, 6:31 a.m.