fastGenoGAM: A GAM based framework for analysis of ChIP-Seq data

Description Usage Arguments Details Value Author(s)

A function to write the data.table of peaks into a narrowPeaks or broadPeaks file

1	writeToBEDFile(peaks, file = NULL)

`peaks`	A data.table or data.frame of peaks as produced by 'callPeaks'
`file`	A file name without suffix. It will be determined automatically. If no file is given, it will be written to a generic 'peaks_[timestamp]' file in the current working directory

Note, the narrow peak calling process does not yet implement any functionality for estimating the start and end of a peak region. Thus the start and end is taken as -100 and +100 around the peak summit. This is mostly an arbitrary choice. A more statistical approach is in development.

Nothing. A narrowPeaks or broadPeaks file written to 'file'

Georg Stricker georg.stricker@in.tum.de

gstricker/fastGenoGAM documentation built on May 17, 2019, 8:56 a.m.