LUAD_CaseStudy_ugs: Genomic event matrix derived from variants found in a cohort...

In saezlab/SLAPenrich: Sample-population Level Analysis of Pathway enrichments

Description

A sparse integer matrix where column names are sample identifiers, and the row names official HUGO gene symbols. A non-zero entry in position i,j of this matrix indicates the number of somatic point mutations harbored by the j-sample in the i-gene. This matrix summarizes the somatic variants of a cohort of 188 lung adenocarcinoma patients of a public available dataset (see source). In this matrix the gene names are updated to recent HUGO nomenclatures.

Format

A named integer matrix with HUGO official gene symbols as row names and sample identifiers as column names: i.e. format: num [1:356, 1:163] 1 0 0 0 0 0 0 0 0 0 ...

- attr(*, "dimnames")=List of 2

..$ : chr [1:356] "ABL1" "ABL2" "ACVR1B" "ACVR1C" ... ..$ : chr [1:163] "16770" "16646" "17741" "16915" ...

Source

The dataset from which this matrix was derived has been studied in Ding et al, 2008. The variant annotations used to assemble this matrix are in Supplementary Table 2 of this publication (available at http://genome.wustl.edu/pub/supplemental/tsp_nature_2008/)

References

Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008;455:1069-75.

See Also

LUAD_CaseStudy

saezlab/SLAPenrich documentation built on May 29, 2019, 12:57 p.m.