chipseq_hooks: Hook functions to extract ChIP-Seq peak data
In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Hook functions to extract ChIP-Seq peak data

1	chipseq_hooks(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE)

`...`	Arguments for the parameters, see "details" section
`RESET`	reset to default values
`READ.ONLY`	whether only return read-only options
`LOCAL`	switch local mode

This hook defines how to get sample ids for a specific marks and how to get peak regions by given mark type and sample id:

sample_id: how to extract sample ids. The argument is the name of the mark and it returns a vector of sample ids.
peak: how to get peak regions. The argument is the name of the mark and a single sample id. The function returns a GRanges object.
chromHMM: how to get chromHMM data. The argument is a single sample id and the function returns a GRanges object. Note the first column in meta columns should be the chromatin states.

Hook functions

Zuguang Gu <z.gu@dkfz.de>

1 2	# There is no example NULL

eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.

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