sig_filter: Filter LINCS Level 5 by Condition

In yduan004/signatureSearch_data: Datasets for signatureSearch package

Filter LINCS Level 5 by Condition

Description

Function to filter Level 5 data from LINCS by specific conditions, such as compound concentrations and treatment times.

Usage

sig_filter(meta, pert_type = "trt_cp", dose, time = "24 h")

Arguments

meta	tibble containing experimental conditions of LINCS data
pert_type	perturbation type, 'trt_cp' refers to treatment ('trt') with compound ('cp'). Description of other perturbation types ('pert_type') can be found in the GEO CMap LINCS User Guide v2.1 URL: https://docs.google.com/document/d/1rbHBy3DKekFm9lZouRG-ZcfLmCsfkUKzGPxxjqxPlYw/edit#
dose	concentration of compound used for treatment, needs to match elements in 'pert_idose' column of 'meta'
time	compound treatment time, needs to match elements in 'pert_itime' column of 'meta'

Value

tibble

Examples

meta <- data.frame(pert_idose=c("2 um","4 um", "10 um"), 
                   pert_itime="24 h",
                   pert_type="trt_cp", pert_iname=c("p1","p2","p3"),
                   cell_id="MCF7")
sig_filter(meta, dose="2 um")

yduan004/signatureSearch_data documentation built on April 7, 2023, 5:02 a.m.