summarize_compound: Summarize query results and annotations by perturbation

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Summarize query results and annotations by perturbation

Description

Takes a data.frame with one row per signatures and summarizes to one row per compound.

Usage

summarize_compound(query_table, is_genetic = FALSE, ntop = 1500)

Arguments

query_table	data.frame of perturbation correlations and annotations.
is_genetic	is query_table from L1000 genetic perts?
ntop	Integer indicating the number of rows to keep after sorting by arrange_by.

Details

Variables related to individual signatures (cell line, dose, duration, and sample number) are pasted together and added as a list to 'title' column. Query correlation values are also added as a list to the 'Correlation' column.

Clinical status is summarized by keeping the most advanced phase only (e.g. Launched > Phase 3). For all other variables, all unique entries are paste together seperated by '|'.

Value

data.frame of perturbation correlations and annotations summarized by perturbation.

hms-dbmi/drugseqr documentation built on Oct. 26, 2024, 6:13 p.m.