cmap_rank: Cmap Rank Signature Database

Description Details References Examples

Description

CMap2 (Version build02) contains GESs for 1,309 drugs and eight cell lines that were generated with Affymetrix Gene Chips as expression platform. In some cases this includes drug treatments at different concentrations and time points. For consistency, the CMap2 data was reduced to drug treatments with concentrations and time points that are comparable to those used for the LINCS data. CMap2 data can be downloaded from GEO or its project site either in raw format or as rank transformed matrix. The ranks are based on DEG analyses of drug treatments (drug vs. no-drug) where the resulting Z-scores were used to generate the rank matrix. The latter was used here and is referred to as rankMatrix. The Affymetrix probe set identifiers stored in the row name slot of this matrix were translated into gene identifies. To obtain a matrix with unique gene identifiers, the ranks for genes represented by more than one probe set were averaged and then re-ranked accordingly. This final gene level rank matrix, referred to as cmap_rank, contains rank profiles for 12,403 genes from 1,309 compound treatments in up to 5 cells corresponding to a total of 3,587 treatment signatures. This matrix can be used for all GESS methods in the signatureSearch package that are compatible with rank data, such as the gess_cmap method.

Details

The cmap_rank data can be downloaded from Bioconductor’s ExperimentHub as HDF5 file. Since CMap2 is much smaller than LINCS, it can be imported in its entirety into a SummarizedExperiment object without excessive memory requirements as shown in the Examples section.

The loaded cmap_rank data object is generated from the rankMatrix downloaded from the CMap project site. For documentation and code of generating the cmap_rank databases from sources, please refer to the vignette of this package by running browseVignettes("signatureSearchData") in R.

References

CMap project site: https://portals.broadinstitute.org/cmap

Examples

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library(ExperimentHub)
# eh <- ExperimentHub()
# query(eh, c("signatureSearchData", "cmap_rank"))
# cmap_rank_path <- eh[["EH3225"]]
# rhdf5::h5ls(cmap_rank_path)

yduan004/signatureSearchData documentation built on Nov. 13, 2019, 1:37 p.m.