readVEGAS: Read a VEGAS gene list
In alexploner/VEGAStools: Basic manipulations of VEGAS gene lists

Description Usage Arguments Details Value See Also

Reads a text file containing output generated by the VEGAS software

1	readVEGAS(fn, path = ".", adjPermP = TRUE, p.adjust = "holm")

`fn`	Name of the file tor read
`path`	Path to file, defaults to `.`
`adjPermP`	FLag indicating whether to adjust the permutation p-values reported by VEGAS, see below. Defaults to `TRUE`.
`p.adjust`	The multiple testing adjustment for the gene-wise p-values; can be any the methods in `p.adjust.methods` except for `none`.

VEGAS returns permutation p-values that are exactly zero, which is of course impossible. The read-in function adjusts this by including the observed test statistic in the null-count.

A data frame containing the data with extra class attribute VEGAS. This is a straightforward wrapper for the raw data, except for the extra column with adjusted p-values, with is named adjPvalue.<adjustment method>.

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alexploner/VEGAStools documentation built on May 10, 2019, 8:57 a.m.