CELLector.CFEs.HMSid_decode: Decoding table for hypermethylated gene promoter cancer...

In najha/CELLector: Genomics guided selection of cancer cell lines

Decoding table for hypermethylated gene promoter cancer functional events

Description

A table with identifiers of cancer functional events (CFEs) involving informative hypermehtylated gene promoters (hms) defined by [1].

Usage

data("CELLector.CFEs.HMSid_decode")

Format

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

Details

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.

Author(s)

Francesco Iorio ([e-mail])

References

[1] Iorio, F. et al. A Landscape of Pharmacogenomic Interactions in Cancer. Cell 166, 740–754 (2016).

See Also

CELLector.CellLine.BEMs_v2, CELLector.PrimTum.BEMs_v2, CELLector.hms_look_up

Examples

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)

najha/CELLector documentation built on Sept. 4, 2024, 10:17 p.m.