inst_filter: Filter LINCS Level 3 by Condition

In yduan004/signatureSearchData: Datasets for signatureSearch package

Filter LINCS Level 3 by Condition

Description

Function to filter Level 3 data from LINCS by specific conditions, such as compound concentrations and treatment times.

Usage

inst_filter(
  meta,
  pert_type = "trt_cp",
  dose = 10,
  dose_unit = "um",
  time = 24,
  time_unit = "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_dose' column of 'meta'
dose_unit	unit of dose of compound treatment, needs to match elements in 'pert_dose_unit' column of 'meta'
time	compound treatment time, needs to match elements in 'pert_time' column of 'meta'
time_unit	unit of time, needs to match elements in 'pert_time_unit' column of 'meta'

Value

tibble

Examples

meta <- data.frame(pert_dose=c(2,4,10), pert_dose_unit="um", 
                   pert_time=24, pert_time_unit="h",
                   pert_type="trt_cp", pert_iname=c("p1","p2","p3"),
                   cell_id="MCF7")
inst_filter(meta)

yduan004/signatureSearchData documentation built on April 7, 2023, 4:12 a.m.