CELLector.createAllSignatures_Partitioned | R Documentation |
This function takes in input the partitioned CELLector search space encoded as a navigable table in a data frame. The signature rule is already derived to defined the paritioned space and extracted here in the same format of CELLector.createAllSignatures
CELLector.createAllSignatures_Partitioned(NavTab)
NavTab |
A CELLector searching space partitioned encoded as a navigable table in data frame format, as returned by the |
A list with two vectors of strings and two numerical vector. Each element of the first two vectors represent a signature of cancer functional events (CFEs, defined in [1]) corresponding to a group in the CELLector searching space partitioned. This is expressed as a logic formula (rule), which a cancer patient's genome must satisfy in order to be included in the group under consideration. The first vector (S
) contains decoded signatures, i.e. where the CFEs involving copy number alterations are represented by a genomic loci and contained cancer driver genes. The second vector (ES
) contains signatures of CFEs as they are represented in the binary event matrix containing the patients genomic data used to build the CELLector searching space. Further deatils are provided in [2]. The third vector (STS
) contains the percentage of cancer patients belonging to the group represented by the signatures. The fourth vector (SC
) contains the number of cancer patients from the cohort belonging to the group.
Lucia Trastulla and Francesco Iorio
[1] Iorio, F. et al. A Landscape of Pharmacogenomic Interactions in Cancer. Cell 166, 740–754 (2016).
[2] Najgebauer, H. et al. Genomics Guided Selection of Cancer in vitro Models.
https://doi.org/10.1016/j.cels.2020.04.007
CELLector.Build_Search_Space_Partitioned
CELLector.createAllSignatures
data(CELLector.PrimTum.BEMs) data(CELLector.Pathway_CFEs) data(CELLector.CFEs.CNAid_mapping) data(CELLector.CFEs.CNAid_decode) data(CELLector.HCCancerDrivers) data(CELLector.CellLine.BEMs) ### Change the following two lines to work with a different cancer type tumours_BEM<-CELLector.PrimTum.BEMs$COREAD CELLlineData<-CELLector.CellLine.BEMs$COREAD ### unicize the sample identifiers for the tumour data tumours_BEM<-CELLector.unicizeSamples(tumours_BEM) ### building a CELLector searching space focusing on three pathways ### and TP53 wild-type patients only CSS_p <- CELLector.Build_Search_Space_Partitioned(ctumours = t(tumours_BEM), verbose = FALSE, minGlobSupp = 0.05, cancerType = 'COREAD', pathwayFocused = c("RAS-RAF-MEK-ERK / JNK signaling", "PI3K-AKT-MTOR signaling", "WNT signaling"), pathway_CFEs = CELLector.Pathway_CFEs, cnaIdMap = CELLector.CFEs.CNAid_mapping, cnaIdDecode = CELLector.CFEs.CNAid_decode, cdg = CELLector.HCCancerDrivers, subCohortDefinition='TP53', NegativeDefinition=TRUE) ### derive signatures from searching space Signatures <- CELLector.createAllSignatures_Partitioned(CSS_p$partitioned) data.frame(Signatures = Signatures$S,'SubType Size'=Signatures$STS, 'SubType Count'=Signatures$SC)
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