| Type: | Package |
| Title: | Extract Drugs from Differential Expression Data from LINCS Database |
| Version: | 0.3.0 |
| Maintainer: | Mohamed Soudy <MohmedSoudy2009@gmail.com> |
| Description: | Get Drug information from given differential expression profile. The package search for the bioactive compounds from reference databases such as LINCS containing the genome-wide gene expression signature (GES) from tens of thousands of drug and genetic perturbations (Subramanian et al. (2017) <doi:10.1016/j.cell.2017.10.049>). |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| Imports: | stringr, gprofiler2, scales, ggplot2, gridExtra, ggpubr |
| Depends: | signatureSearch, signatureSearchData |
| URL: | https://github.com/MohmedSoudy/DFD |
| BugReports: | https://github.com/MohmedSoudy/DFD/issues |
| RoxygenNote: | 7.2.3 |
| NeedsCompilation: | no |
| Packaged: | 2025-02-11 13:23:00 UTC; mohamed.soudy |
| Author: | Mohamed Soudy [aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2025-02-11 13:50:11 UTC |
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
IDs that are converted from gene symbols to ENTREZ gene ids
Author(s)
Mohamed Soudy Mohmedsoudy2009@gmail.com
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 |
Value
re-ranked drug data frame based on their number of targets
Author(s)
Mohamed Soudy Mohmedsoudy2009@gmail.com
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 |
Value
significant drugs data frame that contains list of drugs with their targets
Author(s)
Mohamed Soudy Mohmedsoudy2009@gmail.com
Filter the drug based on the tested cell-line
Description
The function is used to re-rank drugs based on their targets
Usage
get_pert_by_type(perts, perts_type = c("cancer", "Normal"), high_targets = TRUE)
Arguments
perts |
drugs data frame returned by 'get_drugs' function |
perts_type |
type of drug, whether it's from a normal or cancerous cell line |
high_targets |
Boolean paramter to rank their drugs per the number of targets |
Value
re-ranked drug data frame based on their number of targets and cell line
Author(s)
Mohamed Soudy Mohmedsoudy2009@gmail.com
Parse the perturbagens to find out their frequency of occurrence.
Description
The function is used to parse drugs based on their targets
Usage
parse_perts(perts)
Arguments
perts |
drugs data frame returned by 'get_drugs' function |
Value
re-ranked drug data frame based on their number of targets and cell line
Author(s)
Mohamed Soudy Mohmedsoudy2009@gmail.com
Visualise the number of perturbagens and the top activities
Description
The function is used to provide a handy visualization of the top activities
Usage
plot_activities(perts, top = 10, directorypath = NULL)
Arguments
perts |
drugs data frame returned by 'get_drugs' function or 'get_pert_by_type' function |
top |
Number of activities to be visualised (N) The default value is set to 10. |
directorypath |
path to save the output figure |
Value
re-ranked drug data frame based on their number of targets and cell line
Author(s)
Mohamed Soudy Mohmedsoudy2009@gmail.com
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
list containing up_regulated and down_regulated genes ENTREZ gene ids
Author(s)
Mohamed Soudy Mohmedsoudy2009@gmail.com
Read Gene Symbols from CSV file into up and down regulated lists
Description
The function is used to read symbols from a CSV file. The gene symbols should be in the first column
Usage
read_id(csv_path)
Arguments
csv_path |
absolute path of CSV file containing gene symbols and sign |
Value
list containing up_regulated and down_regulated genes symbols
Author(s)
Mohamed Soudy Mohmedsoudy2009@gmail.com
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 |
Value
significant drug data frame after the re-ranking step
Author(s)
Mohamed Soudy Mohmedsoudy2009@gmail.com