Downloads metadata if not available
getCMapConditions(
metadata,
cellLine = NULL,
timepoint = NULL,
dosage = NULL,
perturbationType = NULL,
control = FALSE
)Data frame (CMap metadata) or character (respective filepath)
Character: cell line (if NULL, all values are loaded)
Character: timepoint (if NULL, all values are loaded)
Character: dosage (if NULL, all values are loaded)
Character: type of perturbation (if NULL, all
perturbation types are loaded)
Boolean: show controls for perturbation types?
List of conditions in CMap datasets
Other functions related with the ranking of CMap perturbations:
as.table.referenceComparison(),
filterCMapMetadata(),
getCMapPerturbationTypes(),
loadCMapData(),
loadCMapZscores(),
parseCMapID(),
plot.perturbationChanges(),
plot.referenceComparison(),
plotTargetingDrugsVSsimilarPerturbations(),
prepareCMapPerturbations(),
print.similarPerturbations(),
rankSimilarPerturbations()
if (FALSE) { # \dontrun{
cmapMetadata <- loadCMapData("cmapMetadata.txt", "metadata")
} # }
getCMapConditions(cmapMetadata)
#> $perturbationType
#> [1] "Peptides and other biological agents (e.g. cytokine)"
#>
#> $cellLine
#> [1] "HEPG2"
#>
#> $dosage
#> [1] "0 ng/mL" "0.01 ng/mL" "0.03 ng/mL" "0.1 ng/mL" "0.15 ng/mL"
#> [6] "0.2 ng/mL" "0.3 ng/mL" "0.5 ng/mL" "1 ng/mL" "1.65 ng/mL"
#> [11] "2 ng/mL" "5 ng/mL" "10 ng/mL" "15 ng/mL" "16 ng/mL"
#> [16] "20 ng/mL" "25 ng/mL" "30 ng/mL" "40 ng/mL" "50 ng/mL"
#> [21] "80 ng/mL" "100 ng/mL" "150 ng/mL" "200 ng/mL" "250 ng/mL"
#> [26] "400 ng/mL" "500 ng/mL" "800 ng/mL" "1000 ng/mL" "2000 ng/mL"
#> [31] "2500 ng/mL" "3000 ng/mL" "5000 ng/mL" "8300 ng/mL" "10000 ng/mL"
#> [36] "50000 ng/mL" "100000 ng/mL" "200000 ng/mL"
#>
#> $timepoint
#> [1] "2 h"
#>