Load CMap data (if not found, file will be automatically downloaded)
loadCMapData(
file,
type = c("metadata", "geneInfo", "zscores", "compoundInfo"),
zscoresID = NULL
)Character: path to file
Character: type of data to load (metadata,
geneInfo, zscores or compoundInfo)
Character: identifiers to partially load z-scores file
(for performance reasons; if NULL, all identifiers will be loaded)
Metadata as a data table
If type = "compoundInfo", two files from
The Drug Repurposing Hub will be downloaded containing information
about drugs and perturbations. The files will be named file with
_drugs and _samples before their extension, respectively.
Other functions related with the ranking of CMap perturbations:
as.table.referenceComparison(),
filterCMapMetadata(),
getCMapConditions(),
getCMapPerturbationTypes(),
loadCMapZscores(),
parseCMapID(),
plot.perturbationChanges(),
plot.referenceComparison(),
plotTargetingDrugsVSsimilarPerturbations(),
prepareCMapPerturbations(),
print.similarPerturbations(),
rankSimilarPerturbations()
# Load CMap metadata (data is automatically downloaded if not available)
cmapMetadata <- loadCMapData("cmapMetadata.txt", "metadata")
#> Loading CMap metadata from cmapMetadata.txt...
# Load CMap gene info
loadCMapData("cmapGeneInfo.txt", "geneInfo")
#> cmapGeneInfo.txt not found: downloading data...
#> Extracting cmapGeneInfo.txt.gz...
#> Loading CMap gene information from cmapGeneInfo.txt...
#> pr_gene_id pr_gene_symbol
#> <int> <char>
#> 1: 780 DDR1
#> 2: 7849 PAX8
#> 3: 2978 GUCA1A
#> 4: 2049 EPHB3
#> 5: 2101 ESRRA
#> ---
#> 12324: 4034 LRCH4
#> 12325: 399664 MEX3D
#> 12326: 54869 EPS8L1
#> 12327: 90379 DCAF15
#> 12328: 60 ACTB
#> pr_gene_title
#> <char>
#> 1: discoidin domain receptor tyrosine kinase 1
#> 2: paired box 8
#> 3: guanylate cyclase activator 1A
#> 4: EPH receptor B3
#> 5: estrogen related receptor alpha
#> ---
#> 12324: leucine-rich repeats and calponin homology (CH) domain containing 4
#> 12325: mex-3 RNA binding family member D
#> 12326: EPS8 like 1
#> 12327: DDB1 and CUL4 associated factor 15
#> 12328: actin, beta
#> pr_is_lm pr_is_bing
#> <int> <int>
#> 1: 1 1
#> 2: 1 1
#> 3: 0 0
#> 4: 0 1
#> 5: 0 1
#> ---
#> 12324: 0 1
#> 12325: 0 1
#> 12326: 0 1
#> 12327: 0 1
#> 12328: 0 1
if (FALSE) {
# Load CMap zscores based on filtered metadata
cmapMetadataKnockdown <- filterCMapMetadata(
cmapMetadata, cellLine="HepG2",
perturbationType="Consensus signature from shRNAs targeting the same gene")
loadCMapData("cmapZscores.gctx.gz", "zscores", cmapMetadataKnockdown$sig_id)
}