CELLector.CFEs.HMSid_decode | R Documentation |
A table with identifiers of cancer functional events (CFEs) involving informative hypermehtylated gene promoters (hms) defined by [1].
data("CELLector.CFEs.HMSid_decode")
A data frame with 731 observations (one for each hms CFE) on the following 7 variables.
Cancer.Types
A TCGA label indicating the cancer type where the hms has been identified as informative (as explained in [1])
Genomic.Coordinates
The genomic coordinates of the CgP island whose methylation signal was considered in [1] for this hms
Discretization.threshold
Threshold used to determine the status of this CgP island (hypermethylated or non hypermethylated) defined as the best separative ones between distributions of hypermethylated and non hypermethylated samples when looking at the methylation (beta) signal of the CgP island under consideration in cancer patients, whole procedure described in [1]
dip.statistic
Dip statistic resulting from testing the bimodality of the methylation (beta) signal of the CgP island under consideration in cancer patients. Whole procedure described in [1]
dip.pval
Dip p-value from testing the bimodality of the methylation (beta) signal of the CgP island under consideration in cancer patients. Whole procedure described in [1]
GN
Gene whose promoter is considered by the hms
hms_id
Alphanumerical identifiers of the hms
This data frame contains the annotation of the CFEs involving the hms appearing in the BEMs of cell lines and primary tumours, contained in the CELLector.CellLine.BEMs_v2
and the CELLector.PrimTum.BEMs_v2
data objects (version 2).
This table is used by the CELLector.hms_look_up
function to decode the identifier of CFE involving an hms.
Francesco Iorio (fi9232@gmail.com)
[1] Iorio, F. et al. A Landscape of Pharmacogenomic Interactions in Cancer. Cell 166, 740–754 (2016).
CELLector.CellLine.BEMs_v2
, CELLector.PrimTum.BEMs_v2
, CELLector.hms_look_up
data(CELLector.CFEs.HMSid_decode) head(CELLector.CFEs.HMSid_decode) data(CELLector.CellLine.BEMs_v2) colnames(CELLector.CellLine.BEMs_v2$COREAD)[162] CELLector.hms_look_up(hms_ID = colnames(CELLector.CellLine.BEMs_v2$COREAD)[162], TCGALabel = 'COREAD', hmsId_decode = CELLector.CFEs.HMSid_decode)
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