File conversions

Function to convert a narrowPeak or broadPeak MACS2 file into a GRanges object

Function to convert a GRanges object to a dataframe

Function to convert a GRanges object to a SAF

peak2Granges(peakfile, broad = FALSE)

Granges2df(gr, ignore.strand = FALSE)

Granges2saf(gr)

Arguments

peakfile	Path to MACS2 peak file in narrowPeak or broadPeak format
broad	Logical specifying whether broad or narrowpeak
gr	GRanges object to convert
ignore.strand	Logical indicating whether strand information should be included

Value

GRanges object of peak regions

A dataframe created from the GRanges object

A SAF file created from the GRanges object

Examples

# NOT RUN {
peaks <- peak2Granges("peaks/sample.narrowPeak")
# }