Package 'DFD'

Title: Extract Drugs from Differential Expression Data
Description: Extract Drugs from Differential Expression Data using the Connectivity Map (CMAP) Approach and Library of Integrated Network-Based Cellular Signatures (LINCS) Database.
Authors: Mohamed Soudy [aut, cre]
Maintainer: Mohamed Soudy <[email protected]>
License: GPL-3
Version: 0.1.0
Built: 2024-11-16 09:19:39 UTC
Source: https://github.com/mohmedsoudy/dfd

Help Index

Convert Gene Symbols to ENTREZ IDs

Description

The function is used to convert gene symbols to entrez ids and map the genes to human orthologs

Usage

convert_id(gene_symbols)

Arguments

gene_symbols

gene symbols

Value

ENTREZ gene ids

Author(s)

Mohamed Soudy [email protected]

Examples

convert_id(c("TP53", "A2M"))

Re-rank drugs based on the number of targets

Description

The function is used to re-rank drugs based on their targets

Usage

filter_drugs(drug_frame)

Arguments

drug_frame

drugs data frame returned by 'get_drugs' function

Author(s)

Mohamed Soudy [email protected]

Get Drugs associated with the differential expression profile

Description

The function is used to get list of drugs that are associated with differential expression profile

Usage

get_drugs(up_regulated, down_regulated)

Arguments

up_regulated

up-regulated genes returned by 'prepare_ids' function
down_regulated

down-regulated genes returned by 'prepare_ids' function

Author(s)

Mohamed Soudy [email protected]

Prepare IDs for CMAP Search

Description

The function is used to prepare the ids for the CMAP search

Usage

prepare_ids(up_regulated, down_regulated)

Arguments

up_regulated

up regulated gene symbols
down_regulated

down regulated gene symbols

Value

ENTREZ gene ids

Author(s)

Mohamed Soudy [email protected]

Read Gene IDs from CSV file

Description

The function is used to read IDs from a CSV file

Usage

read_id(csv_path)

Arguments

csv_path

absolute path of CSV file containing gene symbols and sign

Value

up_regulated and down_regulated genes

Author(s)

Mohamed Soudy [email protected]

Run the main pipeline for getting drugs from differentail expression profile

Description

The function is used to run the main pipeline by extracting the drug list given differential expressed genes

Usage

run_pipeline(degs_path, output_path = NULL)

Arguments

degs_path

path to csv file containing degs see example file at https://raw.githubusercontent.com/MohmedSoudy/datasharing/master/differential-expression.csv
output_path

absolute path to output directory

Author(s)

Mohamed Soudy [email protected]